Spin torque oscillator (sto) sensors used in nucleic acid sequencing arrays and detection schemes for nucleic acid sequencing

ABSTRACT

Disclosed herein are methods and apparatuses for sequencing nucleic acids using a detection device, the detection device comprising a plurality of spin torque oscillators (STOs) and at least one fluidic channel. In some embodiments of a method, a nucleotide precursor is labeled with a magnetic nanoparticle (MNP), and the labeled nucleotide precursor is added to the fluidic channel of the detection device. It is determined whether at least one of the plurality of STOs is generating a signal. Based at least in part on the determination of whether the at least one of the plurality of STOs is generating the signal, it is determined whether the labeled nucleotide precursor has been detected.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. application Ser. No.16/791,759, filed Feb. 14, 2020 and entitled “SPIN TORQUE OSCILLATOR(STO) SENSORS USED IN NUCLEIC ACID SEQUENCING ARRAYS AND DETECTIONSCHEMES FOR NUCLEIC ACID SEQUENCING”, which claims the benefit of U.S.Provisional Application No. 62/833,161, filed Apr. 12, 2019 and entitled“SPIN TORQUE OSCILLATOR (STO) SENSORS USED IN NUCLEIC ACID SEQUENCINGARRAYS AND DETECTION SCHEMES FOR NUCLEIC ACID SEQUENCING.” Both of theabove referenced applications are hereby incorporated by reference intheir entireties for all purposes.

BACKGROUND Field of the Disclosure

Embodiments of the present disclosure generally relate tomagnetoresistive (MR) sensor arrays for detection of molecules coupledto magnetic nanoparticles (MNPs), such as for nucleic acid sequencingsuch as deoxyribonucleic acid (DNA) sequencing, and methods of usingsuch MR sensor arrays for molecule detection.

Description of the Related Art

Current state-of-the-art sequencing systems are based on fluorescencesignal detection and provide throughputs of 20 billion reads per run(www.illumina.com/systems/sequencing-platforms/novaseq.html). Achievingsuch performance, however, can require large-area flow cells,high-precision free-space imaging optics, and expensive high-powerlasers to generate sufficient fluorescence signals for successful basedetection.

One type of nucleic acid sequencing used for DNA sequencing is known as“sequencing by synthesis” (SBS). SBS involves binding ofprimer-hybridized template DNA, incorporation of a deoxynucleosidetriphosphate (dNTP), and detection of incorporated dNTP. Gradualincreases in SBS throughput have been accomplished in two ways, thefirst being an outward scaling, where the size and the number of flowcells in the sequencers is increased. This approach increases both thecost of reagents and the price of the sequencing system, as morehigh-power lasers and high-precision nano-positioners must be employed.The second approach involves inward scaling, where the density of DNAtesting sites is increased so that the total number of sequenced DNAstrands in a fixed-size flow cell is higher. To accomplish inwardscaling, increasingly higher numerical aperture (NA) lenses must beemployed to distinguish the signal from neighboring fluorophores as thespacing between them decreases. However, this approach cannot beimplemented indefinitely, as the Rayleigh criterion puts the distancebetween resolvable light point sources at 0.61λ/NA, constraining theminimum distance between two sequenced DNA strands to be no smaller thanapproximately 400 nm. Similar resolution limits apply to sequencingdirectly on top of imaging arrays (similar to cell phone cameras), wherethe smallest pixel size achieved so far is approximately 1(www.ephotozine.com/article/complete-guide-to-image-sensor-pixel-size-29652).

The Rayleigh criterion currently represents the fundamental limitationfor inward scaling of optical SBS systems, which can only be overcome byapplying super-resolution imaging techniques (see A. M. Sydor, K. J.Czymmek, E. M. Puchner, and V. Mannella, “Super-Resolution Microscopy:From Single Molecules to Supramolecular Assemblies,” Special Issue:Quantitative Cell Biology, Vol. 25, 730, 2015) and has not yet beenachieved in highly multiplexed systems. Hence, increasing throughput anddecreasing cost of optical SBS sequencers has been slow due to the needto build bigger flow cells and implement more expensive optical scanningand imaging systems.

Therefore, there is a need for new and improved apparatuses for andmethods of detecting the presence of molecules such as nucleic acidsthat overcome the limitations of conventional apparatuses and methods.

SUMMARY

This summary represents non-limiting embodiments of the disclosure.

Disclosed herein are apparatuses and methods of using magnetic particlesand magnetic sensors comprising spin torque oscillators (STOs) toperform molecule detection, such as for nucleic acid sequencing (e.g.,DNA sequencing using SBS chemistry methods).

Disclosed herein are improved detection devices, systems, and methodsthat use magnetic nanoparticles (MNPs) to allow molecules (e.g., nucleicacids) to be identified. The disclosures herein include embodimentshaving sensors with STOs that allow for detection of characteristicsindicating the presence or absence of MNPs near sensors. Also disclosedherein are detection method embodiments that can be used to detect(e.g., measure or obtain) characteristics or changes in characteristicsgenerated by the sensors indicative of the presence or absence of MNPs(e.g., in response to a magnetic field generated, or not generated, by amagnetic nanoparticle label). For example, devices and methods maydetermine whether a sensor is or is not generating a signal having afrequency at a particular frequency or within a specified range offrequencies, and, based thereon, determine whether one or more MNPs arebeing detected by the sensor. As another example, devices and methodsmay detect a change in a signal generated, or not generated, by a sensorand, based thereon, determine whether one or more MNPs are beingdetected by the sensor.

In some embodiments, a detection device comprises a sensor comprising aSTO, at least one fluidic channel configured to receive molecules to bedetected, wherein at least some of the molecules to be detected arelabeled by MNPs, and detection circuitry coupled to the sensor, whereinthe sensor is encapsulated by a material separating the sensor from theat least one fluidic channel, a surface of the material providingbinding sites for the molecules to be detected, and the detectioncircuitry is configured to detect presence or absence of magnetizationoscillations of the STO in a specified frequency band in response topresence or absence of at least one MNP coupled to one or more bindingsites associated with the sensor. In some embodiments, the at least oneMNP is superparamagnetic or ferromagnetic. The detection circuitry mayinclude analog components (e.g., amplifiers, mixers, envelope detectors,etc.), digital components (e.g., digital signal processors or any othertype of processor, etc.), components that convert signals between theanalog and digital domains (e.g., analog-to-digital converters, etc.),or a combination of these components.

In some embodiments, the detection circuitry is configured to detect thepresence or absence of the magnetization oscillations of the STO in thespecified frequency band by, in part, applying a DC current to the STO.

In some embodiments, a magnetization of the STO is configured tooscillate in the specified frequency band in the absence of the at leastone MNP and to fail to oscillate in the specified frequency band in thepresence of the at least one MNP. In other embodiments, a magnetizationof the STO is configured to oscillate in the specified frequency band inthe presence of the at least one MNP and to fail to oscillate in thespecified frequency band in the absence of the at least one MNP.

In some embodiments, a magnetization of the STO is configured tooscillate in the specified frequency band in the absence of the at leastone MNP and to oscillate in a different frequency band in the presenceof the at least one MNP, the different frequency band being disjointfrom the specified frequency band. In other embodiments, a magnetizationof the STO is configured to oscillate in the specified frequency band inthe presence of the at least one MNP and to oscillate in a differentfrequency band in the absence of the at least one MNP, the differentfrequency band being disjoint from the specified frequency band.

In some embodiments, the detection circuitry comprises asuper-heterodyne detection circuit. In some such embodiments, thesuper-heterodyne detection circuit comprises a reference oscillatorconfigured to generate a reference signal, and a mixer coupled to theSTO, wherein the mixer is configured to mix a signal output from the STOwith the reference signal to produce an output signal for processing. Insome embodiments having a reference oscillator, a frequency of thereference signal is substantially equal to an expected oscillationfrequency of the STO, the expected oscillation frequency being withinthe specified frequency band. In some embodiments, a frequency of thereference signal is selectable, and the detection circuitry is furtherconfigured to select the frequency of the reference signal tosubstantially match an expected oscillation frequency of the STO in thepresence of the at least one MNP. In some embodiments, a frequency ofthe reference signal is selectable, and the detection circuitry isfurther configured to select the frequency of the reference signal tosubstantially match an expected oscillation frequency of the STO in theabsence of the at least one MNP.

In some embodiments, the reference oscillator is a first referenceoscillator, and the reference signal is a first reference signal at afirst frequency that is substantially equal to an expected oscillationfrequency of the STO in response to presence of one or more MNPs of afirst MNP type, and the super-heterodyne circuit further comprises asecond reference oscillator configured to generate a second referencesignal at a second frequency, the second frequency being substantiallyequal to an expected oscillation frequency of the STO in response to thepresence of one or more MNPs of a second type, and a switch coupled to afirst input of the mixer and configured to couple either the firstreference oscillator or the second reference oscillator to the firstinput of the mixer.

In some embodiments, the detection circuitry further comprises aradio-frequency (RF) amplifier, a filter coupled to and disposed betweenthe STO and an input of the RF amplifier, and a diode or envelopedetector coupled to an output of the mixer. In some such embodiments,the RF amplifier is coupled to and disposed between an output of thefilter and an input to the mixer. In some such embodiments, the filteris a high-pass filter or a band-pass filter. In some embodiments, thefilter is a first filter, and the detection circuitry further comprisesa second filter coupled to the output of the mixer, and an additionalamplifier coupled to and disposed between an output of the second filterand an input of the diode or envelope detector. In some suchembodiments, the second filter is a low-pass filter or a band-passfilter.

In some embodiments, the detection circuitry comprises a referenceoscillator coupled to the STO, a processor (e.g., a digital signalprocessor (DSP)), an analog-to-digital converter (ADC) coupled to aninput of the processor, and a low-pass or band-pass filter coupled to aninput of the ADC and configured to filter a signal output from the STOand the reference oscillator to generate a signal to be processed by theADC and the processor. In some such embodiments, the sensor is a firstsensor and the STO is a first STO, and the detection device furthercomprises a second sensor comprising a second STO, the second sensorbeing encapsulated by the material separating the second sensor from theat least one fluidic channel. In some such embodiments, the detectioncircuitry is further configured to detect presence or absence ofmagnetization oscillations of the second STO in the specified frequencyband in response to presence of absence of at least one MNP coupled toone or more binding sites associated with the second sensor, and thereference oscillator is also coupled to the second STO.

In some embodiments, the detection circuitry comprises a directradio-frequency RF ADC, a digital signal processor coupled to an outputof the direct RF ADC, and a high-pass or band-pass filter disposedbetween and coupled to the STO and an input of the direct RF ADC.

In some embodiments, the detection circuitry comprises an amplifiercoupled to the STO, an ADC coupled to an output of the amplifier, and aprocessor (e.g., a DSP) coupled to an output of the ADC. In some suchembodiments, the processor is configured to execute machine-executableinstructions, that, when executed, cause the processor to identify thepresence of the magnetization oscillations of the STO within thespecified frequency band. In some embodiments, the detection circuitryfurther comprises one or more of (a) a high-pass filter disposed betweenthe STO and the amplifier, (b) a band-pass filter disposed between theSTO and the amplifier, (c) a mixer having first and second inputs and anoutput, the first input being coupled to the output of the amplifier,the second input being coupled to an output of a reference oscillator,and the output of the mixer being coupled to an input of the ADC, (d) alow-pass filter disposed between the output of the amplifier and theinput of the ADC, or (e) a band-pass filter disposed between the outputof the amplifier and the input of the ADC.

In some embodiments including a processor and an ADC, the processor isconfigured to execute machine-executable instructions that, whenexecuted, cause the DSP to receive, from the ADC, samples of a signalgenerated by the STO, apply a Fourier transform to the samples, anddetermine whether a result of the Fourier transform indicates thepresence or absence of magnetization oscillations of the STO in thespecified frequency band in order to detect the presence or absence ofmagnetization oscillations of the STO in the specified frequency band.

In some embodiments, the detection circuitry comprises a processor(e.g., a DSP) and an ADC disposed between the STO and the processor. Insome such embodiments, the ADC is configured to provide samples of asignal generated by the STO to the processor, and the processor isconfigured to execute machine-executable instructions that, whenexecuted, cause the processor to perform a frequency-domain analysis ofthe samples to detect the presence or absence of magnetizationoscillations of the STO in the specified frequency band.

In some embodiments, the STO comprises a pinned layer, a free layer, anda spacer layer disposed between the pinned layer and the free layer. Insome such embodiments, the pinned layer comprises one or moreferromagnetic (FM) layers. In some embodiments, the one or more FMlayers are first one or more FM layers, and the free layer comprisessecond one or more FM layers. In some embodiments, the spacer layercomprises an insulating layer or a metal layer. In some embodiments, atequilibrium, a magnetic moment of the free layer is orientedsubstantially co-linearly with a magnetic moment of the pinned layer. Insome embodiments, at equilibrium, a magnetic moment of the free layer isoriented substantially parallel to or anti-parallel to a magnetic momentof the pinned layer. In some embodiments, at equilibrium, a magneticmoment of the free layer is oriented at an angle to a magnetic moment ofthe pinned layer, wherein the angle is between approximately 20 degreesand approximately 60 degrees.

Also disclosed herein is a method of sequencing nucleic acid using adetection device comprising a plurality of STOs and at least one fluidicchannel. In some embodiments, the method comprises labeling a nucleotideprecursor with a MNP, adding the labeled nucleotide precursor to thefluidic channel of the detection device, determining whether at leastone of the plurality of STOs is generating a signal, and based at leastin part on the determination of whether the at least one of theplurality of STOs is generating the signal, determining whether thelabeled nucleotide precursor has been detected. In some embodiments,determining whether the at least one of the plurality of STOs isgenerating the signal comprises detecting a presence or absence of asignal at an output of a super-heterodyne circuit coupled to the atleast one of the plurality of STOs. In some embodiments, determiningwhether at least one of the plurality of STOs is generating a signalcomprises determining whether at least one of the plurality of STOs isgenerating a signal within a specified frequency band.

In some embodiments, the method further comprises binding at least onenucleic acid strand to a binding site in the fluidic channel, andadding, to the fluidic channel, an extendable primer and a plurality ofmolecules of nucleic acid polymerase before adding the labelednucleotide precursor to the fluidic channel of the detection device.

In some embodiments, the method further comprises recording (a) anidentity of the nucleotide precursor, or (b) an identity of a basecomplementary to the labeled nucleotide precursor in response todetermining that the labeled nucleotide precursor has been detected.

In some embodiments, a method of sequencing nucleic acid using adetection device comprising a plurality of STOs and at least one fluidicchannel comprises labeling a first nucleotide precursor with a first MNPtype, the first MNP type selected to cause a magnetization of each ofthe plurality of STOs to oscillate at a first frequency, labeling asecond nucleotide precursor with a second MNP type, the second MNP typeselected to cause the magnetization of each of the plurality of STOs tooscillate at a second frequency, adding the labeled first and secondnucleotide precursors to the fluidic channel of the detection device,detecting a frequency of a signal generated by at least one of theplurality of STOs, determining whether the frequency of the signalgenerated by the at least one of the plurality of the STOs matches thefirst frequency or the second frequency, and, in response to thedetermining, identifying whether the first nucleotide precursor or thesecond nucleotide precursor has been detected.

In some embodiments, detecting the frequency of the signal generated bythe at least one of the plurality of STOs comprises collecting samplesof the signal generated by the at least one of the plurality of STOs,and applying a Fourier transform to the samples. In some embodiments,detecting the frequency of the signal generated by the at least one ofthe plurality of STOs comprises collecting samples of the signalgenerated by the at least one of the plurality of STOs, and determiningfrequency content of the samples.

In some embodiments, detecting the frequency of the signal generated bythe at least one of the plurality of STOs comprises mixing the signalgenerated by the at least one of the plurality of STOs with a firstreference signal of approximately the first frequency, and mixing thesignal generated by the at least one of the plurality of STOs with asecond reference signal of approximately the second frequency. In somesuch embodiments, determining whether the frequency of the signalgenerated by the at least one of the plurality of the STOs matches thefirst frequency or the second frequency comprises identifying thefrequency of the signal generated by the at least one of the pluralityof STOs as the first frequency in response to a result of the mixingbeing greater than a first threshold, and identifying the frequency ofthe signal generated by the at least one of the plurality of STOs as thesecond frequency in response to a result of the mixing being greaterthan the first threshold or a second threshold.

In some embodiments, determining whether the frequency of the signalgenerated by the at least one of the plurality of the STOs matches thefirst frequency or the second frequency comprises determining whetherthe frequency of the signal generated by the at least one of theplurality of STOs is approximately the first frequency or approximatelythe second frequency.

In some embodiments, an apparatus for molecule detection comprises atleast one fluidic channel, a plurality of STOs, each of the plurality ofSTOs configured to generate a RF signal in response to detecting a MNPlabeling a molecule to be detected within the at least one fluidicchannel, means for determining that at least one of the plurality ofSTOs is generating the RF signal, and means for determining, in responseto determining that the at least one of the plurality of STOs isgenerating the RF signal, that the molecule to be detected has beendetected. In some such embodiments, the means for determining that theat least one of the plurality of STOs is generating the RF signalcomprises a super-heterodyne circuit coupled to the at least one of theplurality of STOs.

In some embodiments, an apparatus for molecule detection comprises atleast one fluidic channel, a plurality of STOs, each of the plurality ofSTOs configured to cease to generate a RF signal in response todetecting a MNP labeling a molecule to be detected within the at leastone fluidic channel, means for determining that at least one of theplurality of STOs is not generating the RF signal, and means fordetermining, in response to determining that the at least one of theplurality of STOs is not generating the RF signal, that the molecule tobe detected has been detected. In some embodiments, the means fordetermining that the at least one of the plurality of STOs is notgenerating the RF signal comprises a super-heterodyne circuit coupled tothe at least one of the plurality of STOs.

BRIEF DESCRIPTION OF THE DRAWINGS

So that the manner in which the above-recited features of the presentdisclosure can be understood in detail, a more particular description ofthe disclosure is in reference to embodiments, some of which areillustrated in the appended drawings. It is to be noted, however, thatthe appended drawings illustrate only typical embodiments of thisdisclosure and are therefore not to be considered limiting of its scope,for the disclosure may admit to other equally effective embodiments.

FIG. 1A illustrates a portion of a sensor in accordance with someembodiments.

FIG. 1B illustrates an exemplary sensor that can take advantage of spintorque oscillations to sense a localized magnetic field caused by amagnetic particle in accordance with some embodiments.

FIG. 1C shows an exploded schematic view of a sensor's reference layerand free layer in accordance with some embodiments.

FIGS. 2A, 2B, and 2C illustrate how electrons in an electric currentinteract with thin-film ferromagnetic layers in accordance with someembodiments.

FIGS. 3A, 3B, and 3C illustrate operating principles of STO-basedsensors in accordance with some embodiments.

FIGS. 4A, 4B, and 4C illustrate an apparatus for molecule detection inaccordance with some embodiments.

FIGS. 5A, 5B, 5C, and 5D illustrate portions of another exemplaryapparatus for molecule detection in accordance with some embodiments.

FIG. 5E illustrates a sensor selection approach in accordance with someembodiments.

FIG. 5F illustrates another sensor selection approach in accordance withsome embodiments.

FIGS. 6A, 6B, and 6C illustrate a cross-point array architecture ofsensor elements in accordance with some embodiments.

FIG. 7A illustrates an exemplary super-heterodyne circuit for moleculedetection in accordance with some embodiments.

FIG. 7B illustrates another exemplary super-heterodyne circuit formolecule detection in accordance with some embodiments.

FIGS. 8A and 8B illustrate exemplary detection circuits includinganalog-to-digital converters (ADCs) in accordance with some embodiments.

FIG. 9 illustrates an exemplary in-sensor mixing circuit in accordancewith some embodiments.

FIG. 10 illustrates an exemplary parallel array operation detectioncircuit in which a reference oscillator is coupled to multiple STOs inaccordance with some embodiments.

FIG. 11 illustrates an exemplary method suitable for DNA sequencingusing a single MNP type in accordance with some embodiments.

FIG. 12A illustrates a method suitable for DNA sequencing usingMNP-labeled nucleotide precursors and a tunable reference oscillator inaccordance with some embodiments.

FIG. 12B illustrates a method suitable for DNA sequencing usingMNP-labeled nucleotide precursors and a plurality of referenceoscillators in accordance with some embodiments.

FIG. 13A illustrates a method of manufacturing a detection device inaccordance with some embodiments.

FIG. 13B illustrates the results of each step of the fabrication processof FIG. 13A in accordance with some embodiments.

To facilitate understanding, identical reference numerals have beenused, where possible, to designate identical elements that are common tothe figures. It is contemplated that elements disclosed in oneembodiment may be beneficially utilized on other embodiments withoutspecific recitation.

DETAILED DESCRIPTION

Disclosed herein are improved detection devices, systems, and methodsthat use magnetic nanoparticles (MNPs) to allow molecules (e.g., nucleicacids) to be identified. The disclosures herein include embodimentshaving sensors with spin torque oscillators (STO) that allow fordetection of characteristics indicating the presence or absence of MNPsnear sensors. Also disclosed herein are detection method embodimentsthat can be used to detect (e.g., measure or obtain) characteristics orchanges in characteristics generated by the sensors indicative of thepresence or absence of MNPs (e.g., in response to a magnetic fieldgenerated, or not generated, by a magnetic nanoparticle label). Forexample, devices and methods may determine whether a sensor is or is notgenerating a signal having a frequency at a particular frequency orwithin a specified range of frequencies, and, based thereon, determinewhether one or more MNPs are being detected by the sensor. As anotherexample, devices and methods may detect a change in a signal generated,or not generated, by a sensor and, based thereon, determine whether oneor more MNPs are being detected by the sensor.

As used herein, the term “spin torque oscillator” and acronym “STO”refer to any device that takes advantage of spin-torque-inducedprecession of magnetization caused by spin polarized currents.

In some embodiments, MNPs are coupled to molecules to be detected. Forexample, in DNA sequencing applications, the MNPs may label nucleotideprecursors that are then incorporated into a target DNA strand affixedto a binding site in the vicinity of a sensor. As a result of theincorporation of a MNP-labeled nucleotide precursor, at least one MNP isin the vicinity of the sensor, and its presence can have an impact onthe behavior of the STO. This impact can be detected to detect thepresence of the MNP. Presence of the MNP can then be used to determinethat a particular nucleotide precursor has been incorporated into thetarget DNA strand.

In some embodiments, the STO sensors are designed to oscillate at aselected frequency in the presence of a MNP when a bias current isapplied to the STOs. Molecules to which MNPs are coupled can then bedetected by determining whether the STO is oscillating or notoscillating at the selected frequency. A super-heterodyne detectioncircuit with a reference oscillator having a frequency approximately thesame as the selected frequency may be used to detect whether the STO isoscillating at the selected frequency.

In some such embodiments used for DNA sequencing, a single type of MNPcan label different nucleotide precursors. A single-strand DNA to besequenced can be coupled to a binding site near a sensor having a STO,and a first nucleotide precursor, labeled by the MNP type, can beintroduced. If the first nucleotide precursor is incorporated, the STOoscillates at the selected frequency when a bias current is applied,which allows the incorporated nucleotide precursor to be identified.After a chemistry step to cleave and wash away the magnetic label andprepare the DNA strand for the next base pairing, a second nucleotideprecursor, labeled by the same MNP type, can be introduced, and thedetection procedure repeated. By repeating this process for each of thefour nucleotide precursors, each labeled by a the same MNP type, the DNAstrand can be sequenced.

In some embodiments, the STOs are designed to oscillate at a selectedfrequency in the absence of a MNP when a bias current is applied. Aprocedure similar to the above-described procedure can then be used forDNA sequencing applications, but incorporation of a nucleotide precursoris detected from a lack of oscillation at the selected frequency.

In some embodiments, the STO oscillates at different frequencies inresponse to different MNP types when a bias current is applied. Forexample, the magnetic field generated by a first MNP type may cause theSTO to oscillate at a first frequency, and the magnetic field generatedby a second MNP type may cause the STO to oscillate at a secondfrequency. By determining the frequency of STO oscillations, one candetermine whether the first MNP type is present, whether the second MNPtype is present, or whether neither the first nor second MNP type ispresent.

In some such embodiments used for DNA sequencing, different types ofMNPs can label different nucleotide precursors. A single-strand DNA tobe sequenced can be coupled to a binding site near a sensor with a STO,and all four nucleotide precursors, each labeled by a different MNPtype, can be introduced. If the first nucleotide precursor, labeled by afirst MNP type, is incorporated, the STO oscillates at a first frequencywhen a bias current is applied. If the second nucleotide precursor,labeled by a second MNP type, is incorporated, the STO oscillates at asecond frequency when the bias current is applied, and so forth. Bydetecting the frequency at which the STO oscillates, the identity of theincorporated nucleotide precursor can be determined, and the DNA strandcan be sequenced.

In the following, reference is made to embodiments of the disclosure. Itshould be understood, however, that the disclosure is not limited tospecific described embodiments. Instead, any combination of thefollowing features and elements, whether related to differentembodiments or not, is contemplated to implement and practice thedisclosure. Furthermore, although embodiments of the disclosure mayachieve advantages over other possible solutions and/or over the priorart, whether or not a particular advantage is achieved by a givenembodiment is not limiting of the disclosure. Thus, the followingaspects, features, embodiments and advantages are merely illustrativeand are not considered elements or limitations of the appended claimsexcept where explicitly recited in one or more claims. Likewise,reference to “the disclosure” shall not be construed as a generalizationof any inventive subject matter disclosed herein and shall not beconsidered to be an element or limitation of the appended claims exceptwhere explicitly recited in a claim.

It is to be understood at the outset that the disclosures herein may beused to detect any type of molecule to which a magnetic particle can beattached. The disclosure presumes that the particles attached to themolecules to be detected are magnetic nanoparticles, but thispresumption is exemplary and is not intended to be limiting. Thus, theterm “magnetic nanoparticle” includes all types of magnetic particlesthat can be attached to molecules to be detected.

Any molecule type that can be labeled by a magnetic nanoparticle may bedetected using the devices and methods disclosed herein. Such moleculetypes may be biologic molecule types, such as proteins, antibodies, etc.For example, the disclosures herein may be used to detect nucleic acids(e.g., in DNA sequencing). The disclosures herein may also be used todetect non-biologic (inorganic or non-living) molecules, such ascontaminants, minerals, chemical compounds, etc. The presentation of thedisclosure in the context of nucleic acid sequencing is solely exemplaryand is not intended to limit the scope of the present disclosure.Accordingly, although some of the disclosure herein is provided in thecontext of nucleic acid sequencing, and specifically DNA sequencing, itis to be understood that the embodiments herein generally may be used todetect any type of molecule to which a magnetic nanoparticle can beattached.

Furthermore, although the description herein focuses on DNA as anexemplary nucleic acid, the various embodiments described can be appliedto nucleic acid sequencing in general. Similarly, although SBS is usedfor illustrative purposes in the following description, the variousembodiments are not so limited to SBS sequencing protocols (e.g.,dynamic sequencing could be used instead).

Conventional nucleic acid sequencing, such as that used for DNAsequencing, typically relies on the detection of fluorescence.Specifically, fluorescence-based technologies used to differentiatebetween different bases in a sample (e.g., in fluorescence-based nucleicacid sequencing technologies) rely on, for example, the quality of asignal generated by a detection moiety that is associated with aparticular type of nucleotide. For example, conventional fluorescentsequencing technologies utilize identifiably-distinct fluorescentmoieties, each attached to one of the four nucleotides A, T, C, and Gthat are utilized in a sequencing reaction.

One conventional method of DNA sequencing involves adaptingsingle-strand DNA (ssDNA) for attachment to a solid support of asequencing apparatus and amplifying the quantity of the ssDNA usingtechniques such as the polymerase chain reaction to create many DNAmolecules with a short leader. An oligo complementary to the shortleader may then be added so that there is a short section ofdouble-stranded DNA (dsDNA) at the leader. The double stranded portionof the bound molecule is a primer for a suitable DNA polymerase, suchas, for example, Taq polymerase, which is operable at high temperatures.

The sequencing can then take one of several approaches. For example, thesequencing can use a mixture of four fluorescently-labeled 3′-blockeddNTPs (fluorescently labeled dideoxynucleotide terminators), where thefluorescent label is part of the 3′-blocking group. The fluorescentlabel serves as a “reversible terminator” for polymerization. Each ofthe NTPs is labeled by a different label (i.e., each of the A, G, C, andT nucleotides has a different fluorescent label), and the differentlabels are distinguishable by fluorescent spectroscopy or by otheroptical means.

Four fluorescently-labeled nucleotide precursors can be used to sequencemillions of clusters of DNA strands in parallel. DNA polymerasecatalyzes the incorporation of fluorescently-labeled dNTPs into a DNAtemplate strand during sequential cycles of DNA synthesis. In eachsequencing cycle, the bound double strand DNA molecule is exposed to DNApolymerase and a mixture of the four fluorescently-labeled 3′-blockedNTPs. The polymerase adds one of the four dNTPs to the growingoligonucleotide chain (whichever dNTP is complementary to the nextunpaired base in the ssDNA). The unincorporated dNTPs and otherimpurities that are either left unreacted or generated during thereactions are then separated from the vicinity of the support-bound DNAby washing at a temperature that prevents the free dNTPs from binding tothe ssDNA but is not so high as to dehybridize the dsDNA.

Because only one of the four types of dNTP will have been added to theoligonucleotide, and the four fluorescent labels are distinguishable,the identity of the incorporated dNTP can be identified through laserexcitation and imaging. Specifically, each of four filters is used todetermine whether light of a particular wavelength (e.g., color) isemitted. The fluorescent label can then be enzymatically cleaved toallow the next round of incorporation. Because each base type can pairwith one and only one other base type, the identity of the just-pairedbase in the unknown sequence of the ssDNA is known from the identity ofthe incorporated dNTP (which is known from the wavelength of emittedlight). Thus, the base is identified directly from fluorescencemeasurements during each cycle.

One disadvantage of the above-described approach is that a complicatedoptics system is needed to filter out different wavelengths of light todetect the fluorescent labels of the incorporated dNTPs and todistinguish between the different emitted colors (wavelengths). Otherapproaches have been developed to simplify the optics system, but theyare slower to sequence and require intermediate chemistry steps withineach sequencing cycle. Thus, these approaches have been introduced insmaller, less expensive entry-level sequencing systems but not inhigher-level systems requiring fast throughput.

As explained previously, the disclosures herein may be used to detectany type of molecule (e.g., biologic, organic, inorganic, or non-living)to which a magnetic particle (e.g., a MNP) can be attached. Apparatusesand methods disclosed herein use MNPs and sensors to perform detectionof molecules, such as in nucleic acid sequencing (e.g., DNA sequencingusing SBS chemistry methods). Specifically, embodiments of thisdisclosure include sensors comprising STOs that can be used to detectmagnetic fields (or changes in magnetic fields) emitted by MNPs, and,specifically to distinguish between the presence and absence of magneticfields emitted, or not emitted, by MNPs near the sensors. Embodimentsthat use the same MNP type for all molecules to be detected aredisclosed, as are embodiments that use multiple MNP types, each typelabeling a different molecule type. The disclosed embodiments allowdifferent types of molecules to be distinguished.

Embodiments of the present disclosure also include various detectionmethods to obtain or determine (e.g., measure) characteristics of oroutputs from the sensors (e.g., presence or absence of oscillations at aparticular frequency, and/or a change in oscillation frequency) causedby MNPs used as labels being near the sensors. Knowledge of whichparticular molecule type (e.g., in DNA sequencing applications, the typeof nucleotide precursor) to which the particular MNP label has beenattached may then be used to identify the particular molecule type(e.g., in DNA sequencing applications, the last-paired base of the ssDNAstrand that is complementary to the identified nucleotide precursor).

STO Sensors

In some embodiments disclosed herein, a spin torque oscillationmagnetoresistive sensor is provided to sense magnetic fields caused byMNPs coupled to molecules being detected. The sensor is configured todetect a change in, or a presence or absence of, a precessionaloscillation frequency of a magnetization of a magnetic layer to sensethe magnetic field of a MNP. The sensor can include a magnetic freelayer, a magnetic pinned layer, and a non-magnetic layer between thefree and pinned layers. In operation, detection circuitry coupled tothese layers induces an electrical (DC) current through the layers. Spinpolarization of electrons traveling through the sensor causes aspin-torque-induced precession of the magnetization of one or more ofthe layers. The frequency of this oscillation changes in response to amagnetic field generated by a MNP in the vicinity of the sensor. In someembodiments, knowledge of how a particular type of MNP changes thefrequency of oscillations of the sensor allows the oscillation frequencyto be detected to detect the presence, or absence, of the magnetic fieldand, therefore, the MNP. In some embodiments, the effect of a particulartype of MNP on the oscillation frequency of the sensor is known. Forexample, the particular type of MNP may cause the sensor to oscillate ata frequency f1, and the presence or absence of a signal from the sensorat or near the frequency f1 is used to detect the presence or absence ofthe particular type of MNP in the vicinity of the sensor.

FIG. 1A illustrates a tri-layer structure of a sensor 105 in accordancewith some embodiments. The exemplary sensor 105 of FIG. 1 has a bottom108 and a top 109. The sensor 105 comprises a STO, which is a patternedmagnetic device with an active area including three layers, shown inFIG. 1A as two ferromagnetic (FM) layers 106A, 106B separated by anonmagnetic spacer layer 107.

In some embodiments, the FM layers 106A, 106B are engineered to havetheir magnetic moments oriented either substantially in the plane of thefilm or substantially perpendicular to the plane of the film. Suitablematerials for use in the FM layers 106A, 106B include, for example,alloys of Co, Ni, and Fe (sometimes mixed with other elements). Theexample materials described above are merely exemplary and are notintended to be limiting. Materials suitable for use in the FM layers106A, 106B are known to those having ordinary skill in the art.

The nonmagnetic spacer layer 107 may be, for example, a metallicmaterial or combination of metallic materials, such as, for example,copper or silver, in which case the structure is called a spin valve(SV). Alternatively, the nonmagnetic spacer layer 107 may be aninsulator material such as, for example, alumina (also known in the artas aluminum oxide) or magnesium oxide, in which case the structure isreferred to as a magnetic tunnel junction (MTJ). The materialsidentified for the insulator material are merely exemplary and are notintended to be limiting. Materials suitable for use in the nonmagneticlayer 107 are known to those having ordinary skill in the art.

The active region of the sensor 105 lies in the tri-layer structureshown in FIG. 1A. As described further below in the discussion of FIG.1B, additional layers may be added above and below the layers 106A,106B, 107 shown in FIG. 1A to serve various purposes, such as, forexample, interface smoothing, texturing, and protection from processingused to pattern the overall detection device (e.g., as shown anddescribed below in the context of, e.g., FIGS. 4A-4C, 5A-5D, etc.) andpassivation/protection of the sensor 105. Accordingly, a component thatis in contact with a magnetic sensor 105 may be in contact with one ofthe three illustrated layers 106A, 106B, or 107, or it may be in contactwith another part of the sensor 105 that is not illustrated in FIG. 1A.

As described further below, the magnetic moment of one or both FM layers106A, 106B of the sensor 105 can be excited into precessional orbits byapplying an electric current to the device through an effect known asspin transfer. Spin transfer (or spin torque transfer, as it issometimes called) involves the interaction of a spin polarized current(i.e., a current that has some large fraction of electrons with spinsoriented in the same direction) with a FM layer (e.g., 106A, 106B).

FIG. 1B is a view of another exemplary sensor 105 that can takeadvantage of spin torque oscillations to sense a localized magneticfield caused by a magnetic particle (e.g., a MNP). FIG. 1B shows across-sectional view of the sensor 105 with the MNP being sensed shownlocated to the right of the sensor 105.

The exemplary sensor 105 of FIG. 1B includes a sensor stack 304 that issandwiched between optional first and second magnetic shields 306A,306B. If present, the magnetic shields 306A, 306B can be made of anelectrically conductive, magnetic material such as NiFe so that they canfunction as electrical leads as well as magnetic shields. The sensorstack 304 includes a pinned layer structure 311, a free layer 310, and anon-magnetic spacer layer 107 sandwiched between the free layer 310 andthe pinned layer structure 311. As explained above in the context ofFIG. 1A, the non-magnetic spacer layer 107 can be a non-magnetic,electrically conducting spacer layer, or it can be a thin, non-magnetic,electrically-insulating barrier layer. A capping layer 328 (e.g.,comprising tantalum) can be situated adjacent to the free layer 310 asshown in FIG. 1B. It is to be appreciated that FIG. 1B shows the sensor105 with an exemplary orientation of layers (e.g., the pinned layerstructure 311 above the free layer 310), but that other orientations arepossible (e.g., the pinned layer structure 311 can be below the freelayer 310, the sensor 105 can be rotated relative to how it is shown inFIG. 1B, some of the elements shown in FIG. 1B (e.g., shields 306A,306B) can be omitted, etc.).

The pinned layer structure 311 can include a magnetic pinned layer 314,a reference layer 319, and a non-magnetic antiparallel coupling layer321 sandwiched between the pinned layer 314 and the reference layer 319.The pinned and reference layers 314, 319 can comprise a material suchas, for example, CoFe, and the antiparallel coupling layer 321 cancomprise a material such as, for example, Ru having a thickness of, forexample, about 10 Angstroms. The pinned layer 314 can be exchangecoupled with a layer of antiferromagnetic material, AFM layer 312, whichcan comprise a material such as, for example, IrMn, PtMn, or some othersuitable antiferromagnetic material. Exchange coupling between the AFMlayer 312 and the pinned layer 314 strongly pins the magnetization 324of the pinned layer 314 in a first direction as indicated. Strongantiparallel coupling between the pinned and reference layers 314, 319pins the magnetization 326 of the reference layer 319 in a second(antiparallel) direction as indicated.

In the exemplary embodiment shown in FIG. 1B, the free layer 310 has itsmagnetization 330 biased in a direction that is substantiallyanti-parallel to the magnetization 326 of the reference layer 319. Insome embodiments, in the quiescent state of the magnetization (e.g.,when the STO is not oscillating), the magnetization 330 of the freelayer 310 is at a modest angle relative to the magnetization 326 of thereference layer 319. This can be seen with reference to FIG. 1C, whichshows an exploded schematic view of the reference layer 319 and freelayer 310. As shown, the reference layer 319 has a magnetization 326that is pinned in a direction that is parallel (or antiparallel) to anapplied magnetic field 327, but the free layer 310 has a magnetization330 that is biased in a direction that is nearly antiparallel to thedirection of the reference layer magnetization 326, but may be is offsetby an angle 329. The angle 329, if present, is generally about 20-60degrees but may be as large as nearly 90 degrees. Biasing of the freelayer 310 can be provided by hard magnetic bias layers that are notshown in FIG. 1B, but would be into and out of the page in FIG. 1B.While the free layer 310 is magnetically biased, the magnetization 330of the free layer 310 is free to move in a precessional spin torqueoscillation 337 as indicated in FIG. 1B and as discussed previously.

With reference again to FIG. 1C, canting of the free layer 310magnetization 330 direction with respect to the magnetization 326direction of the reference layer 319 can be provided by a magneticanisotropy having a component oriented perpendicular to the direction ofmagnetization 326 of the reference layer 319, and/or perpendicular to adirection of an applied magnetic field 327. This magnetic anisotropy canbe produced by a layer of antiferromagnetic material that is weaklyexchange coupled with the free layer 310, or by shape anisotropy, or bya texture induced magnetic anisotropy. The canting of the free layer 310can also be achieved by placement of high coercivity magnetic materialnear the free layer 310 and with magnetization having a substantialcomponent perpendicular to the reference layer 319, in analogy to thehard bias structures that may be used in recording heads to stabilizethe free layer of GMR and TMR readback sensors. These are by way ofexample, however; other mechanisms could be used as well.

As described in further detail below, when a high current density ofspin-polarized electrons generated by one magnetized layer impinges upona second magnetized layer, spin torque effects are observed, and thesespin torque effects dynamically excite the second layer's magnetizationthrough a mechanism called spin transfer. Here, electrons travelingthrough the ferromagnet tend to have their spins aligned parallel to themagnetization of the ferromagnet, losing any component of spin angularmomentum transverse to the magnetization. To conserve angular momentum,the polarized current must then exert a torque upon the magnetization.

FIGS. 2A through 2C illustrate in further detail how an electron in anelectric current interacts with thin-film FM layers. Quantum mechanicsdictate that the probability is high that an electron interacting with aFM layer will cause the electron spin to be oriented preferentiallyparallel or antiparallel to the direction of the FM layer's moment fortransmitted and reflected electrons respectively. As shown in FIG. 2A,electrons with spin 210, which is parallel to the moment 206 of the FMlayer 204, preferentially pass through the FM layer 204, whereas thosewith spin 208, which is antiparallel to the moment 206 of the FM layer204, preferentially are reflected back. Due to this phenomenon, theinterface between a nonmagnetic (NM) layer 202 (assumed for purposes ofthis explanation to be a metal layer, although, as discussed above, theNM layer 202 may alternatively be an insulator) and a FM layer 204 actsas a spin filter that can act to spin polarize (i.e., make one spindirection more preferential) an incoming electric current.

For a device with two FM layers 224 and 228 separated by a nonmagneticmetal layer 226 (spacer layer), as shown in FIGS. 2B and 2C, an incomingelectric current spin polarized by the first FM layer (FM1) 224interacts differently with the second FM layer (FM2) 228, depending onthe orientation of the second FM layer 228's magnetic moment. If themoments of both FM layers 224 and 228 are parallel to one another (FIG.2B), then many electrons will pass through the device because manyelectrons in the current will have their spin oriented with the momentof the second FM layer 228 (spin 234). Few electrons will be reflectedback (spin 232).

In the opposite case, when the moments of the two FM layers 224 and 228are oriented in an anti-parallel fashion (FIG. 2C), many electrons willbe blocked from passing through the second FM layer 228 (spin 236), andfar fewer electrons will traverse the device (spin 238). This means theamount of current passing through the device is dependent on theorientation of the moments of the two FM layers 224 and 228 with respectto one another. Because the resistance of the device that includes FMlayers 224 and 228 and NM layer 226 is inversely proportional to thecurrent, the resistance of the device is dependent on the orientation ofthe moments of the two FM layers 224 and 228 (i.e., the resistance issmaller when the moments are parallel than it is when they areantiparallel).

Whereas the above description presumes use of a nonmagnetic metal layer226 separating the two FM layers 224 and 228 (a configuration also knownas a spin valve (SV) or giant magnetoresistance (GMR) device), aninsulating layer known as a tunneling barrier can alternatively be usedas the spacer layer (e.g., instead of NM layer 226) separating the FMlayers 224, 228. In such implementations, the spacer layer may be madeof oxide-based material. These types of devices are called magnetictunnel junctions (MTJs), and they exhibit a similar resistance response(referred to as tunnel magnetoresistance or TMR) because of spinpolarized tunneling as opposed to spin filtering.

Referring again to FIG. 1B, with electrons flowing from the referencelayer 319 through the non-magnetic spacer layer 107 to the free layer310, the spin of the electrons flowing through the reference layer 319are polarized by the magnetization 326 of the reference layer 319. Thesepolarized electrons can then apply a torque to the free layermagnetization 330, generating spin waves that result in chaoticmagnetization dynamics (noise) or collective excitations (oscillations),depending on various parameters of the system such as sensor 105 shape,anisotropy, layer materials and thicknesses, and applied currents andmagnetic fields.

As explained above, spin torque oscillations involve spin-torque-excitedprecession of the magnetization along the equilibrium axis of theferromagnet. For example, with reference to FIG. 1B, the precession, oroscillation, of the magnetization 330 is indicated by oscillation 337.Note that although the pinned layer 314 magnetization 324 is constrainedby exchange anisotropy to an antiferromagnetic layer 312, it is possiblefor the magnetization of the pinned layer 314 to oscillate as well, andto contribute to the sensor 105 signal when the applied currentdensities are high enough to generate spin torque excitations in thepinned layer 314.

The frequency of this precession (oscillation frequency) shifts with theapplication of a magnetic field. With a suitable selection of sensormaterials and geometry, this shift can be very large. Frequency shiftsup to 180 GHz/T have been demonstrated, and higher values are possible.Some embodiments described herein take advantage of these frequencyshifts to detect the change in magnetic field at the free layer 310induced by magnetic nanoparticles in the vicinity of the sensor 105.

Referring to FIG. 1B, the sensor 105 is connected via leads 341A, 341Bto processing circuitry 344. The leads 341A, 341B, which may be magneticor nonmagnetic, can be connected with the optional shield/lead layers306A, 306B (if present) such that one lead 341A is connected with onelead/shield layer 306A, while the other lead 341B is connected with theother lead/shield layer 306B. The processing circuitry 344 sends a sense(bias) current through the sensor stack 304 and also measures theelectrical resistance across the sensor stack 304. As those skilled inthe art will appreciate, the electrical resistance across thenonmagnetic spacer layer 107 changes as the orientation of themagnetization 330 of the free layer 310 changes relative to themagnetization 326 of the reference layer 319. The closer thesemagnetizations 330, 326 are to being parallel, the lower the electricalresistance will be. Conversely, the closer these magnetizations 330, 326are to being anti-parallel, the higher the electrical resistance willbe. The resistance of the device effectively acts as amagnetic-field-to-voltage transducer.

The presence of a MNP in the vicinity of the sensor 105 causes theabove-described change in the frequency of the oscillation 337 of themagnetization 330. As the magnetization 330 oscillates, the frequency ofthis oscillation 337 can be measured by the processing circuitry 344 bymeasuring the change of electrical resistance across the sensor stack304. In addition or alternatively, the presence or absence ofoscillation 337 at a particular frequency can be detected to determinewhether a MNP is in the vicinity of the sensor 105. Therefore, inaccordance with some embodiments disclosed herein, the spin torqueoscillation is used to detect the presence or absence of a magneticfield caused by magnetic nanoparticles.

FIGS. 3A through 3C further illustrate the basic operating principles ofSTO-based sensors 105. FIG. 3A shows how incident electrons 904 witharbitrary spin direction either transmit through or are reflected by aFM layer 906. As shown, those incident electrons 904 with spin parallelto the magnetic moment of the FM layer 906 are transmitted electrons908, whereas incident electrons 904 with spin anti-parallel to themagnetic moment of the FM layer 906 are reflected electrons 902. Anyspin angular momentum lost becomes a torque acting on the FM layer 906.The torque from a single electron interaction is small, but for a spinpolarized current on the order of a milli-Ampere, there areapproximately 1015 electrons interacting with the FM layer 906 persecond. Thus, the net torque on the FM layer 906 can be sufficient toinduce the moment into a dynamic mode. These dynamics are governed bythe Landau-Lifshitz-Gilbert-Slonczewski (LLGS) equation:

$\frac{d\hat{m}}{dt} = {{{- \gamma}\hat{m} \times {\overset{\rightarrow}{H}}_{eff}} + {\alpha\hat{m} \times \frac{d\hat{m}}{dt}} + {\frac{\eta I}{❘m❘}\hat{m} \times \hat{p} \times \hat{m}}}$

where γ is the gyromagnetic ratio, {circumflex over (m)} is thenormalized moment vector, {right arrow over (H)}_(eff) is the effectivemagnetic field acting on the FM layer 906, α is the phenomenologicalGilbert damping parameter, η is spin polarization of the current I, and{circumflex over (p)} is the direction of the current's spinpolarization.

The first term in the equation, called the Larmor precession term,indicates that in the absence of any damping, the moment of the FM layer906 will precess around the effective magnetic field acting on the FMlayer 906. However, the second term (Gilbert damping) comes fromintrinsic damping occurring in every ferromagnet that acts to damp outany dynamics of the moment. The final term is the Slonczewski spintorque term that acts like either a damping or anti-damping term,depending on the polarity of the applied electric current. In the caseof anti-damping, the spin torque will entirely cancel out the Gilbertdamping at a sufficient current amplitude and will result inmagnetization oscillations as shown in FIG. 3C. As the current amplitudefurther increases, the oscillation amplitude also increases, eventuallycausing the moment to cross points 90 degrees from equilibrium. In thisregion, the cross product in the Slonczewski term changes sign and actsto damp out the motion such that the moment will rotate 180 degrees fromthe original position, as shown in FIG. 3B.

Thus, considering a full STO device similar to that described above,with one FM layer 906 excited through spin transfer effects and a secondFM layer 906 with a moment fixed in some chosen direction (they areco-linear), a STO excited as shown in FIG. 3C will produce aradio-frequency (RF) voltage signal from an applied DC current due toresistance fluctuations (and, therefore, voltage and currentfluctuations) caused by magnetoresistive effects. The frequency of thegenerated RF signal can be on the order of GHz.

Taking advantage of these operational principles for detection, someembodiments disclosed herein involve an array of sensors 105 comprisingSTO devices, such as the sensors 105 shown in FIGS. 1A, 1B, and 1C andthe arrays shown in, for example, FIGS. 4A-4C, 5A-5D, etc. Each of thesensors 105 of the sensor array may be used to detect magnetic particles(e.g., MNPs) in a fluidic channel of a detection device. Each sensor 105may have dimensions of less than about 30 nm to detect magnetic fieldson the order of a few millitesla (mT). In some embodiments, individualsensors 105 in a sensor array are configured to generate a RF signalonly within a narrow band of magnetic fields (e.g., around zero appliedfield, although that is not required), for example between 50 and −50Oe. In some embodiments, individual sensors 105 in a sensor array areconfigured to generate a RF signal in the presence of larger appliedfields.

In DNA sequencing applications, nucleotide precursors (or, moregenerally, nucleic acids) labeled by MNPs and incorporated by polymerasemay be detected by determining whether the sensor 105 is generating a RFsignal within a specified frequency band. For example, in someembodiments, the sensor 105 generates a RF signal at or near aparticular frequency in the absence of a MNP, but in the presence of aMNP labeling the DNA base (or a nucleotide precursor incorporated in atarget DNA strand being sequenced), the local magnetic field issufficient to “turn off” the STO at and around that frequency (e.g., thelocal magnetic field may shift the frequency of the RF signal). In otherembodiments, the sensor 105 generates a RF signal in the presence of theMNP, but is otherwise “off” in the absence of MNPs. Accordingly, it isto be appreciated that detection may be performed using sensors 105comprising STOs designed to “turn on” and generate a RF signal at aparticular frequency or within a particular frequency band only in thepresence of an applied magnetic field generated by one or more MNPs inthe vicinity of the sensor 105, or to “turn off” and generate a RFsignal at a particular frequency or within a particular frequency bandonly in the absence of an applied magnetic field generated by one ormore MNPs in the vicinity of the sensor 105.

An advantage of performing detection using sensors 105 comprising STOdevices is that the MNPs used as labels may be either superparamagnetic(e.g., thermally unstable such that the magnetic field generatedfluctuates over time) or ferromagnetic. Moreover, the use of STOs doesnot require the moments of individual MNPs to be aligned in the samedirection (e.g., detection may be accomplished without use of anexternal magnetic field). One benefit of superparamagnetic particles isthat they are not ferromagnetic and will not stick to or attract eachother appreciably when introduced into a flow cell of a detection device(e.g., the fluidic channels described below in the context of, e.g.,FIGS. 4A-4C and 5A-5D).

Detection Devices

The STO-based sensors 105 described above may be incorporated into anapparatus for the detection of molecules that are coupled to respectivemagnetic nanoparticles (e.g., for nucleic acid sequencing). FIGS. 4A,4B, and 4C illustrate a detection device 100 that may be used, e.g., fornucleic acid sequencing in accordance with some embodiments. FIG. 4A isa top view of the apparatus, and FIG. 4B is a cross-section view at theposition indicated in FIG. 4A. FIG. 4C is a block diagram showingcomponents of the detection device 100. As shown in FIG. 4A, theexemplary detection device 100 comprises a sensor array 110 thatincludes a plurality of sensors 105, with four sensors 105A, 105B, 105C,and 105D shown in FIG. 4A. (For simplicity, this document refersgenerally to the sensors by the reference number 105. Individual sensorsare given the reference number 105 followed by a letter.) The sensorarray 110 shown in the exemplary embodiment of FIG. 4A is a lineararray.

In some embodiments, each of the plurality of sensors 105 is coupled toat least one line 120 for reading a characteristic of or output from oneor more of the sensors 105 (e.g., detecting whether a sensor 105 isoscillating, determining whether a sensor 105 is oscillating at aparticular frequency, etc.). (For simplicity, this document refersgenerally to the lines by the reference number 120. Individual lines aregiven the reference number 120 followed by a letter.) In the exemplaryembodiment shown in FIG. 4A, each sensor 105 of the sensor array 110 iscoupled to two lines 120. Specifically, the sensor 105A is coupled tothe lines 120A and 120E, the sensor 105B is coupled to the lines 120Band 120E, the sensor 105C is coupled to the lines 120C and 120E, and thesensor 105D is coupled to the lines 120D and 120E. The lines 120A, 120B,120C, and 120D reside under the sensors 105A, 105B, 105C, and 105D,respectively, and the line 120E resides over the sensors 105. FIG. 4Bshows the sensor 105D in relation to the lines 120D and 120E.

The detection device 100 also includes a fluidic channel 115 (which mayalso be referred to as a nanochannel or flow cell) that is adjacent tothe sensor array 110. As its name suggests, the fluidic channel 115 isconfigured to hold fluids (e.g., liquids, gases, plasmas) when thedetection device 100 is in use. The fluidic channel 115 may by open(e.g., if its shape is rectangular, it may have three sides; if itsshape is curved, it may have a shape that is a portion of a cylinder;etc.) or closed (e.g., if its shape is rectangular, it may have foursides; if its shape is curved, it may be cylindrical; etc.). The shapeof the fluidic channel 115 may be regular or irregular along its length.The fluidic channel 115 may be coupled to a device (e.g., a pump) thatforces fluids into the fluidic channel 115. Alternatively, the fluidicchannel 115 may not be coupled to a device that injects or removesfluids.

As shown in FIG. 4B, the fluidic channel 115 has a wall 117 that isadjacent to the sensor array 110. The wall 117 may be referred to as aproximal wall. The wall 117 may be substantially vertical as illustratedin FIG. 4B. Alternatively, the wall 117 may be sloped at least in part(e.g., some or all of the interior of the fluidic channel 115 may be atan angle that is not 90 degrees, or it may be curved (e.g., in the shapeof a portion or all of a cylinder)). In general, the fluidic channel 115and wall 117 may have any shapes that allow the sensors 105 to detectthe presence of magnetic particles on the other side of the wall 117that are within the fluidic channel 115.

When the detection device 100 is in use, the sensors 105 are able todetect, through the wall 117, the presence or absence of magneticnanoparticles (MNPs) that are in the fluidic channel 115. Thus, the wall117 has properties and characteristics that protect the sensors 105 fromwhatever fluid is in the fluidic channel 115 while still allowing thesensors 105 to detect MNPs that are within the fluidic channel 115. Forexample, the material of the wall 117 (and potentially of the rest ofthe fluidic channel 115) may be or comprise an insulator material. Forexample, in some embodiments, a surface of the wall 117 comprisespolypropylene, gold, glass, and/or silicon. In addition, the thicknessof the wall 117 may be selected so that the sensors 105 can detect MNPswithin the fluidic channel 115. In some embodiments, the thickness ofthe wall 117 is between approximately 2 nm and approximately 20 nm.

In some embodiments, the wall 117 has a structure (or multiplestructures) configured to anchor or bind molecules to be sensed (e.g.,nucleic acid or molecules of a nucleic acid polymerase) to the wall 117.For example, the structure (or structures) of the wall 117 may include acavity or a ridge or multiple cavities/ridges that provide binding sitesassociated with the sensors 105.

To simplify the explanation, FIGS. 4A and 4B illustrate an exemplarydetection device 100 with a single fluidic channel 115 and only foursensors 105A, 105B, 105C, 105D in the sensor array 110. It is to beappreciated that the detection device 100 may have many more sensors 105in the sensor array 110, and it may have either additional fluidicchannels 115 or a more intricate single fluidic channel 115 (e.g., witha different shape or with interconnected channels). In general, anyconfiguration of sensors 105 and fluidic channel(s) 115 that allows thesensors 105 to detect MNPs in the fluidic channel(s) 115 may be used.

As illustrated in FIG. 4C, the detection device 100 includes detectioncircuitry 130 coupled to the sensor array 110 via the lines 120. In someembodiments, in operation, the detection circuitry 130 applies a currentto the lines 120 to detect a characteristic of or output from at leastone of the plurality of sensors 105 in the sensor array 110, where thecharacteristic or output indicates a presence or an absence of amagnetically-labeled molecule in the fluidic channel 115. For example,in some embodiments, the characteristic or output is a signal or anabsence of a signal. The detection circuitry 130 may comprise anysuitable components, including, generally, suitable detection circuitry.Such detection circuitry 130 may comprise hardware and/or software. Thedetection circuitry 130 may include, for example, one or more of: aprocessor capable of executing machine-executable instructions, anapplication-specific integrated circuit (ASIC), a controller, aprogrammable circuit (e.g., FPGA), etc.

As an example of a detection device 100 with a larger number of sensors105 in the sensor array 110, FIGS. 5A, 5B, 5C, and 5D illustrateportions of an exemplary detection device 100 that includes severalchannels, one or more of which may be a separate fluidic channel 115 inaccordance with some embodiments, or the aggregation of which may beconsidered a single fluidic channel 115. In the embodiment of thedetection device 100 shown in FIGS. 5A, 5B, 5C, and 5D, the plurality ofsensors 105 of the sensor array 110 is arranged in a rectangular gridpattern. Each of the lines 120 identifies a row or a column of thesensor array 110. It is to be understood that FIGS. 5A, 5B, 5C, and 5Dshow only a portion of the detection device 100 to avoid obscuring theparts of the detection device 100 being discussed. It is to beunderstood that the various illustrated components (e.g., lines 120,sensors 105, fluidic channels 115, etc.) might not be visible in aphysical instantiation of the detection device 100 (e.g., some or allmay be covered by protective material, such as an insulator material).

FIG. 5A is a perspective view of the exemplary detection device 100 inaccordance with some embodiments. The detection device 100 includes ninelines 120, labeled as 120A, 120B, 120C, 120D, 120E, 120F, 120G, 120H,and 120I. It also includes five fluidic channels, labeled as 115A, 115B,115C, 115D, and 115E. As explained above, the fluidic channels 115A,115B, 115C, 115D, and 115E may be considered to be separate fluidicchannels 115 or a single fluidic channel 115. The detection device 100also has a bottom surface 119.

FIG. 5B is a top view of the exemplary detection device 100 from FIG.5A. The lines 120G, 120H, and 120I, which are not visible from the topview, are shown using dashed lines to indicate their locations. Thelines 120A-120F are shown in solid lines but, as explained above, thelines 120A-120F might also not be visible in the top view (e.g., theymay be covered by protective material, such as an insulator material).

FIG. 5C is a cross-sectional view of the detection device 100 along theline labeled “5C” in FIG. 5A. As shown, each of the lines 120A, 120B,120C, 120D, 120E, and 120F is in contact with the top of one of thesensors 105 along the cross-section (namely, line 120A is in contactwith sensor 105A, line 120B is in contact with sensor 105B, line 120C isin contact with sensor 105C, line 120D is in contact with sensor 105D,line 120E is in contact with sensor 105E, and line 120F is in contactwith sensor 105F). The line 120H is in contact with the bottom of eachof the sensors 105A, 105B, 105C, 105D, 105E, and 105F. It is to beappreciated that although FIGS. 5A-5D illustrate the lines 120 incontact with the sensors 105, the lines 120 may, in general, be coupledto the sensors 105 (i.e., they may be directly connected, or there maybe intervening components disposed between the lines 120 and the sensors105).

The sensors 105A and 105B are separated by the fluidic channel 115A(unlabeled in FIG. 5C but shown in FIG. 5A). Similarly, the sensors 105Band 105C are separated by the fluidic channel 115B, the sensors 105C and105D are separated by the fluidic channel 115C, the sensors 105D and105E are separated by the fluidic channel 115D, and the sensors 105E and105F are separated by the fluidic channel 115E. As discussed furtherbelow, either or both of the vertical walls of each fluidic channel 115may be the wall 117.

In some embodiments, each sensor 105 is assigned to a single fluidicchannel 115. For example, in the exemplary device illustrated in FIGS.5A-5D, the sensors 105 coupled to the line 120A may be configured tosense MNPs in the fluidic channel 115A, the sensors 105 coupled to theline 120B may be configured to sense MNPs in the fluidic channel 115B,the sensors 105 coupled to the line 120C may be configured to sense MNPsin the fluidic channel 115C, the sensors 105 coupled to the line 120Dmay be configured to sense MNPs in the fluidic channel 115D, and thesensors 105 coupled to the line 120E may be configured to sense MNPs inthe fluidic channel 115E.

In the exemplary embodiment illustrated in FIGS. 5A-5C, there are morecolumns of sensors 105 than there are fluidic channels 115 (i.e., in theexemplary embodiment shown, there are six columns corresponding to lines120A-120F and only five fluidic channels 115A-115E). In suchembodiments, each vertical wall of one fluidic channel 115 may be thewall 117. In other words, a single fluidic channel 115 may be sensed bytwice as many sensors 105 as each of the other fluidic channels 115. Forexample, in the exemplary embodiment of FIGS. 5A-5D, any of the fluidicchannels 115 may be sensed by two columns of sensors 105. For example,the fluidic channel 115B may be sensed by the sensors 105 coupled toboth lines 120B and 120C. In this example, the sensors 105 coupled tothe line 120A would be assigned to sense the contents of the fluidicchannel 115A, the sensors 105 coupled to the line 120D would be assignedto sense the contents of the fluidic channel 115C, the sensors 105coupled to the line 120E would be assigned to sense the contents of thefluidic channel 115D, and the sensors 105 coupled to the line 120F wouldbe assigned to sense the contents of the fluidic channel 115E.

FIG. 5D is a cross-sectional view of the detection device 100 along theline labeled “5D” in FIG. 5A. As shown, the line 120E is in contact withthe top of each of the sensors 105G, 105E, and 105H along thecross-section. Each of the lines 120G, 120H, and 120I is in contact withthe bottom of one of the sensors 105 along the cross-section (namely,line 120G is in contact with sensor 105G, line 120H is in contact withsensor 105E, and line 120I is in contact with sensor 105H). As explainedabove, the lines 120 shown in FIG. 5D need not be in direct contact withthe sensors 105; instead, they may be connected through interveningcomponents.

In some embodiments (see, e.g., FIGS. 5E, 5F), the detection device 100includes a plurality of selector elements 111, each of which is coupledto a respective one of the sensors 105, where each of the selectorelements 111 exhibits thresholding behavior such that for voltages abovea given value (i.e., Vth) the selector element 111 has highconductivity, and below that voltage the conductivity of the selectorelement 111 is effectively zero. The selector elements 111 may comprise,for example, transistors, diodes, etc. As will be appreciated by thosehaving ordinary skill in the art, different schemes of addressing(selecting) the sensors 105 (individually or in groups) can be used thatensure only the voltage dropped across the intended sensor(s) 105 isabove Vth. Accordingly, selector elements 111 may be used reduce thechances of “sneak” currents that could transmit through neighboringelements and degrade the performance of the detection device 100.

FIG. 5E illustrates an exemplary sensor 105 selection approach inaccordance with some embodiments. In the exemplary embodiment shown inFIG. 5E, a respective selector element 111 (e.g., shown as a CMOStransistor) is coupled in series with the sensor 105. In this exemplaryembodiment, three lines 120A, 120B, and 120C allow a characteristic ofthe sensor 105 to be sensed. Conceptually, the line 120A may beconsidered to be a read-out line, the line 120C may be considered to bea control line, and the line 120B may be considered to be either or botha read-out line and a control line. For more detail on configurationssuch as the exemplary one shown in FIG. 5E, see B. N. Engel, J. Åkerman,B. Butcher, R. W. Dave, M. DeHerrera, M. Durlam, G. Grynkewich, J.Janesky, S. V. Pietambaram, N. D. Rizzo, J. M. Slaughter, K. Smith, J.J. Sun, and S. Tehrani, “A 4-Mb Toggle MRAM Based on a Novel Bit andSwitching Method,” IEEE Transactions on Magnetics, Vol. 41, 132 (2005).

FIG. 5F illustrates another exemplary sensor 105 selection approach inaccordance with some embodiments. In the exemplary embodiment shown inFIG. 5F, a selector element 111 (e.g., a diode or a similar thresholdingelement, as is known in the art, such as semiconductor diodes,operational transconductance amplifiers (OTAs), vanadium oxide layers,capacitive threshold-logic gates, etc.) is deposited “in-stack” togetherwith the magnetic films of the sensors 105 and then placed into across-point architecture. Although FIG. 5F shows the in-stack selectorelements 111 below the sensors 105, it is to be understood that theorder of the in-stack selector elements 111 and the sensors 105 may bereversed. Respective selector devices (e.g., CMOS transistors) may beused to turn on the individual lines 120A, 120B to address/accessindividual sensors 105 in the detection device 100. The use of CMOSselect transistors may be simple due to the prevalence of foundriesavailable to fabricate the front end (i.e., the nanofabrication to buildthe CMOS transistors and underlying circuitry), but the types ofcurrents used for operation may use a cross-point design to eventuallyreach the densities desired. Additional details on configurationssuitable to select sensors 105 (e.g., in cross-point arrays) may befound in C. Chappert, A. Fert, and F. N. Van Daul, “The emergence ofspin electronics in data storage,” Nature Materials, Vol. 6, 813 (2007)and in J. Woo et al., “Selector-less RRAM with non-linearity of devicefor cross-point array applications,” Microelectronic Engineering 109(2013) 360-363.

FIGS. 6A through 6C illustrate an embodiment of a cross-point arrayarchitecture 300 that may be included in the detection device 100 inaccordance with some embodiments. For illustration, the sensors 105illustrated in FIGS. 6A through 6C comprise MTJ elements 308, but it isto be appreciated that, as explained above, some or all of the sensors105 may be spin valves.

Referring to FIG. 6A, the cross-point array architecture 300 includestop wires 318 and bottom wires 320. As shown in the exemplary embodimentof FIG. 6A, the top wires 318 are oriented substantially perpendicularlyto (at approximately 90 degree angles from) the bottom wires 320. Anexample MTJ element 308 (e.g., a sensor 105) is situated between acrossing of the array (dashed circle). The example MTJ element 308includes two or more FM layers 310, 314 separated by one or morenon-magnetic layers 107 (e.g., comprising MgO). As shown, one of the FMlayers is a free layer 310 that will rotate in the presence of amagnetic field, and another of the FM layers is a pinned (or fixed)layer 314 that may be a single FM layer coupled to an AFM layer 312.Alternatively, a compound structure called a synthetic antiferromagnet(SAF) may be used. The SAF includes two FM layers separated by amagnetic coupling layer (e.g., ruthenium), with one of the two FM layerscoupled to an AFM layer. It is to be understood that although theexample layer arrangement of MTJ element 308 shows a general structurewith layers over or under other layers, intervening layers not shown canbe inserted. Moreover, as discussed above, additional layers may bedisposed above and/or below the illustrated structure.

To illustrate some of the features of the cross-point array architecture300, FIG. 6B shows a cross-section of the cross-point array architecture300 along the top wire 318 direction (indicated in FIG. 6A by thedash-dot line labeled “6B”), and FIG. 6C shows a cross-section of thecross-point array architecture 300 along the bottom wire 320 direction(indicated in FIG. 6A by the dashed line labeled “6C”). As shown, thesides of the MTJ elements 308 (the sensors 105) are encapsulated bymaterial 336, which may be an insulator. Optionally, as shown in FIG.6B, a hard bias magnetic material 338 may also be deposited between theMTJ elements 308. In embodiments including hard bias magnetic material338, a thin layer of insulator 340 is also deposited on top of the hardbias magnetic material 338 to electrically insulate it from the topwire(s) 318.

Referring to FIG. 6C, the cross section shows the fluidic channels 115(e.g., nanofluidic or microfluidic channels), which may be, for example,trenches etched in an insulator. As shown, a small amount of insulator322 is left on the sidewalls of the sensors 105 (illustrated as MTJelements 308) so that the MNPs do not electrically interact with thesensors 105. The portion of the insulator exposed to (and forming) thefluidic channel 115 may form the wall 117 to which polymerase moleculesor molecules to be detected (e.g., nucleic acid samples) may be attachedfor detection.

Detection Circuits

Determining the state of the sensor 105 (e.g., determining whether theSTO is oscillating, determining whether it is oscillating at aparticular frequency or within a particular frequency band, determiningat what frequency the STO is oscillating, etc.) can be accomplishedusing various types of detection circuitry.

In some embodiments, determining the state of the sensor 105 isaccomplished using a super-heterodyne detection circuit. Generally,super-heterodyne detection may be used to detect RF signals using afrequency mixing technique that takes a high frequency signal and“down-shifts” it to a much lower frequency (e.g., baseband or anintermediate frequency) at which the signal can be processed moreconveniently. This method involves the use of a non-linear mixer elementthat adds alternating current (AC) voltage signals with the functionalform V_(n) sin (ω_(n)t), where V_(n) and ω_(n) are the peak voltage andfrequency, respectively, of the nth signal. To understand the behaviorof this element, consider the output V_(mix) of a mixer to be a functionof two input signals:

V _(mix) =F(V ₁ sin(ω₁ t)+V ₂ sin(ω₂ t))

Because the mixer is a non-linear element, expanding the summation in apower series produces the expression:

V _(mix)=α₁(V ₁ sin(ω₁ t)+V ₂ sin(ω+t)+α₂(V ₁ ²(sin(ω₁ t))²+2V ₁ V ₂sin(ω₁ t)sin(ω₂ t)+V ₂ ²(sin(ω₂ t))²)+

where terms higher than second order are ignored. Using thetrigonometric identities

${\sin^{2}(x)} = {\frac{1}{2}\left( {1 - {\cos\left( {2x} \right)}} \right)}$

and 2 sin(ω₁t) sin(ω₂t)=cos(ω₁t−ω₂t)−cos(ω₁t+ω₂t), the equation abovemay be simplified into the form:

$V_{mix} = {{\alpha_{1}\left( {{V_{1}{\sin\left( {\omega_{1}t} \right)}} + {V_{2}{\sin\left( {\omega_{2}t} \right)}}} \right)} + {\alpha_{2}\left( {{\frac{V_{1}^{2}}{2}\left\lbrack {1 - {{cos2\omega}_{1}t}} \right\rbrack} + {V_{1}{V_{2}\left\lbrack {{{\cos\left( {\omega_{1} - \omega_{2}} \right)}t} - {\cos\left( {\left( {\omega_{1} + \omega_{2}} \right)t} \right)}} \right\rbrack}} + {\frac{V_{2}^{2}}{2}\left\lbrack {1 - {{cos2\omega}_{2}t}} \right\rbrack}} \right)} + \cdots}$

Ignoring the higher-frequency terms, the mixed signal now consists ofterms with frequencies that are the difference and sum of the originalinput signal frequencies:

V _(mix)=α₂ V ₁ V ₂ cos(ω₁−ω₂)t−a ₂ V ₁ V ₂ cos(ω₁+ω₂)^(t)+

FIG. 7A illustrates an exemplary super-heterodyne detection circuit 600Ain accordance with some embodiments. In the illustrated embodiment, aSTO 604 generates a RF signal (e.g., in response to a magnetic fieldgenerated by a MNP in its vicinity) when the DC bias current 602 isapplied. The frequency of the RF signal generated by the STO 604 (e.g.,in response to the presence or absence of a selected MNP type) can beselected/designed through the choice of materials, dimensions, amplitudeof the applied DC bias current 602, magnetic field, and other variables,as is known in the art.

In the exemplary embodiment of FIG. 7A, the RF signal (e.g., in therange of 1-10 GHz) from the STO 604 is first passed through a high-passor band-pass filter 606 to substantially eliminate from the RF signalany DC signal from the DC bias current 602 used to excite the STO 604.Assuming the STO 604 oscillates at a known frequency with smallvariation, a band-pass filter with the band centered around the STO'soscillation frequency may be used to reduce noise and improve thesignal-to-noise ratio (SNR). A high-pass filter may be used, forexample, if the STO 604's frequency variation is large and/or there arelarge variations of the STO 604's frequency over the sensor array 110(e.g., as shown in FIGS. 4A-4C, 5A-5D, etc.).

As shown in FIG. 7A, the output from the filter 606, which may be on theorder of pico- to nano-Watts of power, is optionally amplified by a RFamplifier 608 and sent to a mixer 612, where a fixed-reference signalfrom a reference oscillator 610 is used to mix the output down to, forexample, frequencies below 100 MHz. The reference oscillator 610 mayproduce a reference signal having a frequency close to that of the STO604. Alternatively, instead of a reference oscillator 610, the source ofthe reference signal can be a reference STO 604 (e.g., substantiallyidentical to the STOs 604 of the sensors 105 in the sensor array 110,but removed from the fluidic channel(s) 115 and physically separatedfrom the sensor array 110) or any other element that generates ahigh-frequency signal at a frequency approximately equal to thefrequency of the signal expected to be generated by the STO 604. Forexample, ring oscillators or other signal generators used invery-large-scale integration (VLSI) designs may be suitable.

In the exemplary embodiment illustrated in FIG. 7A, the output of themixer 612 is then passed through a low-pass or band-pass filter 614 toremove higher-frequency components. As shown in FIG. 7A, the outputsignal from the low-pass or band-pass filter 614 may optionally beamplified by a second amplifier 616. The output signal is then passed toa diode detector circuit 618 (or, e.g., any other suitable circuit thatoperates as an envelope detector), and the envelope of the output signalmay be detected as a DC voltage (output 620).

As will be appreciated by those having ordinary skill in the art, in theexemplary embodiment of FIG. 7A, if there is no input RF signal at theinput to the RF amplifier 608, the output of the mixer 612 (ω₁-ω₂) willalso be approximately zero. Accordingly, the output of the circuit 600Awill be a DC voltage only when the frequency of the RF signal generatedby the STO 604 approximately matches the frequency of the signalgenerated by the reference oscillator 610. Thus, the response of theexemplary super-heterodyne detection circuit 600A to the STO 604changing from being “on” to being “off” would be to go from a finitemeasured voltage to (approximately) zero volts. In other words, thepresence of a non-zero DC output 620 indicates that the STO 604 is “on,”whereas an absence of a DC output 620 (or a DC output 620 below athreshold) indicates that the STO 604 is “off”

It is to be understood that another mode of operation of the exemplarysuper-heterodyne detection circuit 600A is achieved if the STO 604 doesnot “turn off” in response to the presence (or absence) of a MNP in itsvicinity, but instead has its frequency altered sufficiently due to thefield from a MNP such that (ω₁-ω₂) is larger than the cutoff frequencyof the low/band-pass filter 614, which would also result in(approximately) no signal at the DC output 620. In either approach,detecting the presence (or absence) of a MNP label (e.g., tethered to aDNA base (or to an incorporated nucleotide precursor)) can be a binaryoperation where the detection circuitry 130 detects an output voltage inthe absence of a MNP in the vicinity of a sensor 105 and no signal whena NMP is present (or vice versa). This approach allows for rapidevaluation of the presence or absence of MNPs in a large area array 110of sensors 105 comprising STOs 604, which can boost the throughput of adetection system (e.g., for DNA sequencing applications) and increasethe speed of data collection.

As explained previously, some embodiments allow for the detection ofdifferent MNP types, each of which has a distinguishable effect on theoscillation of the STO 604. For example, a first MNP type may cause theSTO 604 to oscillate at a first frequency, a second MNP type may causethe STO 604 to oscillate at a second frequency, a third MNP type maycause the STO 604 to oscillate at a third frequency, and a fourth MNPtype may cause the STO 604 to oscillate at a fourth frequency. In somesuch embodiments, the reference oscillator 610 shown in FIG. 7A may betunable such that the frequency of the signal generated by the referenceoscillator 610 may be, at various times, at or around any of the first,second, third, and fourth frequencies.

Alternatively, the exemplary circuit 600A may be modified as shown inFIG. 7B, in which the single reference oscillator 610 has been replacedby a set of four reference oscillators, 610A, 610B, 610C, and 610Dcoupled to a switch 611. The circuit 600B of FIG. 7B may be used in aDNA sequencing application in which each nucleotide precursor is labeledby a different MNP type, with each MNP type causing the STO 604 togenerate a RF signal having a different frequency (e.g., a first MNPtype causes the STO 604 to oscillate at a first frequency, a second MNPtype causes the STO 604 to oscillate at a second frequency, a third MNPtype causes the STO 604 to oscillate at a third frequency, and a fourthMNP type causes the STO 604 to oscillate at a fourth frequency). Afterall four MNP-labeled nucleotide precursors have been introduced into thefluidic channel 115 of a sequencing device, and enough time has elapsedfor incorporation, the switch 611 may be activated to, in turn, connecteach of the reference oscillators 610A, 610B, 610C, and 610D to themixer 612. The DC output 620 of the circuit 600B should be nonzero onlywhen the reference oscillator 610 associated with the MNP type labelingthe incorporated nucleotide precursor is connected to the mixer 612. Forexample, if the reference oscillator 610A generates a reference signalat a first frequency that is approximately the same as the expectedfrequency at which the STO 604 will oscillate in the presence of thefirst MNP type, and the DC output 620 is nonzero when the switch 611connects the reference oscillator 610A to the mixer 612, it can bededuced that the incorporated nucleotide precursor is the one labeled bythe first MNP type.

In some embodiments having multiple reference oscillators 610 (e.g.,FIG. 7B) or a tunable single reference oscillator 610, the low- orband-pass filer 614 is a low-pass filter having a cutoff frequencyhigher than the highest of the first, second, third, and fourthfrequencies. In other embodiments, the low- or band-pass filter 614 is atunable band-pass filter that can be tuned so that its passbandapproximately centers, at different times, on the first, second, third,and fourth frequencies and, so centered, does not overlap any of theother of the first, second, third, or fourth frequencies.

In some embodiments, the STOs 604 are designed to generate RF signalscharacterized by a large change in frequency due to the magnetic fieldgenerated by the MNPs. Here, the STOs 604 can also be considered to turneither “off” or “on” depending on the choice of reference oscillator 610frequency used in the detection circuits described above. For example,referring to FIG. 7A, if, at equilibrium (i.e., when no MNP is present),the frequency of the signals generated by the STOs 604 is f₁ and thereference oscillator 610 frequency is f₀≈f₁, the frequency of the signalat the output of the mixer 612, namely (f₁−f₀), will be smaller than thecutoff frequency of the low-pass (or band-pass) filter 614 prior to thediode detector 618. A finite voltage can then be read at the output ofthe circuit 600A. When a MNP is present and exerting an additionalmagnetic field on the STO 604, the frequency of the STO 604 changes tof₂, which is either much larger or smaller than f₀. As a result, theoutput of the mixer 612 is strongly attenuated by the low-pass (orband-pass) filter 614, because the signal frequency is (much) higherthan the filter 614's cutoff frequency. Then the output of the detectorcircuit 600A is effectively zero, as in the case described above,without any requirement for a tight band of magnetic field in which STOoscillations occur. It should be noted that once again the response canbe reversed by choosing the reference oscillator 610 frequency to bedifferent from the STO 604 frequency at equilibrium and set to be closeto the STO 604 frequency in the presence of a MNP, so that a signal isonly detected in the presence of a particle.

Note that although FIGS. 7A and 7B show a single STO 604 at the input ofthe super-heterodyne circuit 600A, 600B, in other embodiments anensemble of STOs 604 provides the input into a single detector circuit600A, 600B using, for example, multiplexers. Such embodiments can reducethe footprint consumed by the detection circuitry 130 on a detectiondevice 100 (e.g., a microfluidic chip used for sequencing of nucleicacids). Also envisioned is a separate circuit board or chip to handlesuper-heterodyne detection within a detection system, although thisapproach may increase the latency of the system as well as use signalamplification (e.g., RF amplifier 608 and/or amplifier 616 shown inFIGS. 7A and 7B), which might not be used if the circuit 600A, 600B isincluded on the detection device 100 itself (e.g., a DNA sequencingchip).

FIGS. 8A, 8B, 9, and 10 show additional and/or alternative exemplarydetection circuitry 130 embodiments for detecting the frequency and/orpresence/absence of a signal generated by a STO 604 in accordance withsome embodiments. FIGS. 8A and 8B show two alternative analog-to-digitalconverter (ADC)-based embodiments. Several of the elements of FIGS. 8Aand 8B are identical to those shown in FIGS. 7A and 7B and haveidentical reference numbers. Those elements were described above, andthat discussion applies in the context of FIGS. 8A and 8B and is notrepeated.

The detection circuit 700 of FIG. 8A differs from that of FIGS. 7A and7B in that digital, rather than analog, signal processing is used.Specifically, as shown, the output from the low- or band-pass filter 614is provided as the input to an ADC 626. The output of the ADC 626 isprovided to a digital signal processor (DSP) 628, which can then detectthe frequency of the RF signal using known methods (e.g., by calculatinga fast Fourier transform or by applying any other knownfrequency-analysis technique to assess the frequency content of the RFsignal, etc.). It is to be understood that although FIG. 8A and otherfigures herein illustrate a DSP 628, other components could be used inaddition or instead. For example, the DSP 628 can be augmented orreplaced by components such as a general-purpose processor, anapplication-specific integrated circuit (IC), a microprocessor, acontroller, a programmable logic device, a field-programmable gatearray, or other similar components that are known in the art.Furthermore, although FIG. 8A illustrates many of the same components asFIGS. 7A and 7B, several of these components are optional. For example,the high- or band-pass filter 606, reference oscillator 610, mixer 612,and low- or band-pass filter 614 are optional, and one or more of themmay be omitted from FIG. 8A. As will be appreciated by those havingordinary skill in the art, with the optional mixer 612 and optionalreference oscillator 610 omitted, FIG. 8A allows the frequency of the RFsignal generated by the STO 604 to be detected/measured digitally. Forexample, the DSP 628 may perform a Fourier transform (or any othertechnique to assess the frequency content of the signal) and identifypeaks in the frequency spectrum. The location(s) of the peak(s) may thenbe assessed in view of the expected RF signal frequencies of the MNPtypes being used to identify which, if any, of the MNP types has beendetected.

The detection circuit 710 in FIG. 8B is another digital approach thatuses direct RF conversion. In this exemplary embodiment, the output ofthe high- or band-pass filter 606 is the input to a direct RF conversionADC 630 operating at a high frequency (sampling rate) and with arelatively small bandwidth. The output of the direct RF conversion ADC630 is provided to a DSP 628, which may then detect the frequency of theRF signal generated by the STO 604 using known methods (e.g., bycalculating a fast Fourier transform or by applying any other knownfrequency-analysis technique to assess the frequency content of the RFsignal, etc.). This embodiment may be advantageous in some applicationsbecause the ADC 630 and DSP 628 process the signal withoutdownconversion (e.g., the ADC 630 and DSP 628 process the signal at theRF signal frequency generated by the STO 604). It is noted that in theexemplary embodiment of FIG. 8B, the use of an anti-aliasing filter isoptional due to the limited bandwidth of the STO 604. Optionally, thedetection circuit 710 may additionally include a low noise amplifier.

FIG. 9 shows an exemplary in-sensor mixing circuit 720 for use inaccordance with some embodiments. In other words, at least a portion ofthe circuit 720 may be incorporated into the sensor 105. The circuit 720of FIG. 9 is similar to the circuit 710 of FIG. 8B, except that in FIG.9 a reference oscillator 610 is coupled with the STO 604 before the lowor band-pass filter 632. It is to be understood that although FIG. 9shows an embodiment that uses digital processing, use of in-sensormixing is also contemplated for purely analog detection embodiments suchas those shown in FIGS. 7A and 7B.

FIG. 10 shows another detection circuit 730 in accordance with someembodiments. The circuit 730 is a parallel array operation embodiment inwhich a single reference oscillator 610 is coupled to two or more STOs604 and their associated detection circuits. The exemplary circuit 730of FIG. 10 further extends the concept of FIG. 9 so that the referenceoscillator 610 is shared among two or more STOs 604 and their associatedcircuitries. It is to be appreciated that the embodiments of FIGS. 9 and10 can also be adapted to operate with the configurations shown in FIGS.7A and 7B.

In addition to one or more of the circuits described in the context ofFIGS. 7A-10 , as described above, the detection circuitry 130 mayinclude, for example, a processor configured to executemachine-executable instructions enabling the processor to interpret themeaning of the output of the circuit. In some embodiments in which theoutput of the circuit is an analog signal (e.g., FIG. 7A, FIG. 7B), thedetection circuitry 130 may include an analog-to-digital converterdisposed between the output of the circuit 600A, 600B and a processor.

Detection Methods

The sensors 105 and/or detection devices 100 described above may be usedto detect molecules labeled by MNPs, as described further below.Suitable detection methods include those in which a binary decision(e.g., yes/no, 1/0, etc.) is made as to whether a MNP, and therefore amolecule to which the MNP is coupled, is present in the vicinity of asensor 105. For simplicity, the explanation below is presented in thecontext of DNA sequencing, but, as stated previously, it is to beunderstood that the methods described also may be used in otherapplications and to detect types of molecules other than nucleic acids.

In some embodiments, target molecules to be detected (e.g., nucleic acidstrands to be sequenced) are attached to the walls 117 of the fluidicchannel(s) 115 of a detection device 100. Polymerase may be introducedat this point. For example, the polymerase may be bound (attached orcoupled) to the wall 117 along with a target ssDNA to be sequenced.Nucleotide precursors labeled by MNPs may then be introduced into thefluidic channel(s) 115. The polymerase operates to incorporatecomplementary nucleotide precursors labeled by MNPs into the target DNAstrand. Only the appropriate (complementary) base (i.e., for DNAsequencing, cytosine (C) with guanine (G) or adenine (A) with thymine(T)) will be incorporated, and its presence can be detected by thesensors 105. Assuming this process is done one base pair at a time, thepresence or absence of the MNP labeling the complementary nucleotideprecursor, and therefore the identity of base with which that nucleotideprecursor pairs in the target DNA strand, can be determined using thevarious device embodiments of, for example, FIGS. 4A-5F.

The presence or absence of a MNP in the vicinity of a particular sensor105 can be detected by applying a magnetic field across the sensor 105and applying a bias current to read the sensor 105. The application of amagnetic field across the sensor 105 is optional, but it may bebeneficial in applications in which multiple types of MNPs are present(e.g., in DNA sequencing applications in which different nucleotideprecursors are labeled by different MNP types and multiple nucleotideprecursors are added to the fluidic channel 115 at substantially thesame time). The magnetic field may be applied using an electromagnet,e.g., by placing the pole pieces on either side of the detectiondevice), a distributed coil, a solenoid oriented perpendicular to thefluidic channel 115, etc. to generate the magnetic field in thedirection of the pinned layer 314's moment. The means for generating themagnetic field may be mounted, for example, on the bottom surface 119 ofthe detection device 100. As another example, the means for generating amagnetic field may be included in a system that includes the detectiondevice 100. It is to be understood that other suitable means ofgenerating the magnetic field, such as, for example, by using permanentmagnets or super-conducting magnets, are possible, are specificallycontemplated herein, and are not excluded. The applied magnetic fieldaligns the moments of all of the MNPs in a common direction so that themeasured signals due to the presence of a MNP are similar.

With the free layer excited through spin transfer effects and the fixedlayer with its moment fixed, a STO excited as described above (e.g., inthe context of FIG. 3C) will produce a RF voltage signal from an appliedDC current due to resistance fluctuations caused by magnetoresistiveeffects. Therefore, by connecting the sensors 105 to detectionelectronics/circuitry as described above, the presence and/or absence ofMNPs near the sensors 105 can be detected. In DNA sequencingapplications, for example, nucleotide precursors (or, more generally,nucleic acids) labeled by MNPs and incorporated into a target DNA strandby polymerase may be detected by determining whether the sensor 105 isgenerating a RF signal (e.g., at a specified frequency or within aspecified frequency band), because only in the presence of a MNPlabeling the nucleotide precursor incorporated in a target DNA strandbeing sequenced would the local magnetic field be sufficient to “turnon” (or “turn off,” or shift the oscillation frequency of) the STO.

Methods of molecule detection may use a single MNP type or multiple MNPtypes. FIG. 11 illustrates an exemplary sequential binary method 500suitable for DNA sequencing in which a single MNP type is used to labelall four nucleotide precursors in accordance with some embodiments. FIG.11 is applicable whether the presence of a MNP in the vicinity of asensor 105 causes the STO to “turn on” or “turn off.” It is to beunderstood that FIG. 11 illustrates the procedure for a single sensor105. In embodiments in which a detection device 100 includes a pluralityof sensors 105, some of the steps of the method 500 (e.g., steps 510,512, 514) may be performed independently for each of the plurality ofsensors 105.

At 502, the method 500 begins. At 504, molecules of each the fournucleotide precursors (A, T, C, and G) are all labeled by the same typeof MNP. The different nucleotide precursors, each labeled by the sameMNP type, are then introduced one at a time into, for example, a fluidicchannel 115 of a detection device 100. Thus, at 506, a first nucleotideprecursor to be tested is selected. At 508, the selected(magnetically-labeled) nucleotide precursor is added to the fluidicchannel 115 of a detection device 100. After sufficient time has passedto allow the nucleotide precursor to be incorporated in the target DNAstrands being sequenced, at 510, it is determined whether the STO of aselected sensor 105 is, or is not, generating a RF signal havingspecified characteristics. The characteristics may include, for example,an amplitude and/or frequency.

As explained above, in some embodiments, the STO generates the RF signalin response to one or more MNPs being in its vicinity but otherwise doesnot generate the RF signal. In such embodiments, the presence of one ormore MNPs causes the STO to “turn on.” In other embodiments, the STOgenerates the RF signal in the ordinary course and ceases to generate itin response to one or more MNPs being in its vicinity. In suchembodiments, the presence of one or more MNPs causes the STO to “turnoff” The presence or absence of the RF signal caused by the presence orabsence one or more MNPs can be detected using suitable detectioncircuitry 130, including, for example, the exemplary embodimentsdescribed above in the context of FIGS. 5E, 5F, and 7A-10 .

In embodiments in which MNPs cause the STO to “turn on” (the presence ofthe RF signal indicates the presence of one or more MNPs in the vicinityof the sensor 105), if it is determined at 510 that the STO of theselected sensor 105 is generating a RF signal having the specifiedcharacteristics, then at 512 it is determined that the tested nucleotideprecursor was incorporated into a DNA strand coupled to a binding siteassociated with the sensor 105. The identity of the base with which thetested nucleotide precursor paired (its complement) may then berecorded. If, however, is it determined at 510 that the STO of theselected sensor 105 is not generating a RF signal having the specifiedcharacteristics (interpreted to mean that the previously-testednucleotide precursor was not incorporated at the binding site associatedwith the sensor 105), then at 516 it is determined whether thepreviously-tested nucleotide precursor was the last of the fournucleotide precursors to be tested. If so, then the method ends at 514.If not, the method returns to 506, where the next nucleotide precursorto be tested is selected, and at least steps 508 and 510 are repeated.

In embodiments in which the MNPs cause the STO to “turn off” (theabsence of the RF signal indicates the presence of one or more MNPs inthe vicinity of the sensor 105), if it is determined at 510 that the STOof the selected sensor 105 is not generating a RF signal having thespecified characteristics, then at 512 it is determined that the testednucleotide precursor was incorporated into a DNA strand coupled to abinding site associated with the sensor 105. The identity of the basewith which the tested nucleotide precursor paired (its complement) maythen be recorded. If, however, it is determined at 510 that the STO ofthe selected sensor 105 is generating a RF signal having the specifiedcharacteristics (interpreted to mean that the previously-testednucleotide precursor was not incorporated at the binding site associatedwith the sensor 105), then at 516 it is determined whether thepreviously-tested nucleotide precursor was the last of the fournucleotide precursors to be tested. If so, then the method ends at 514.(Again, it is to be understood that when a detection device 100 includesa plurality of sensors 105, the method 500 may end for some sensor(s)105 but not for others if the DNA fragments being sequenced are notidentical and the base pair to be completed and detected by differentsensors 105 differs.) If not, the method returns to 506, where the nextnucleotide precursor to be tested is selected, and at least steps 508and 510 are repeated.

The method 500 can be performed using one or more sensors 105. It is tobe appreciated that when more than one sensor 105 is used, the decisionat 510 can differ for different sensors 105. For example, in some typesof SBS, a long strand of DNA is (or a plurality of long strands of DNAfrom a single donor organism are) cut into smaller, random-lengthsegments prior to sequencing. All of these smaller strands, which arefrom the same donor, are randomized sub-strands of the complete strandto be sequenced. For example, if the complete strand includes thesequence ATGGCTTAG, the smaller strands could include, for example,distinct sub-strands (e.g., ATGG and TTAG) as well as, if a plurality ofthe longer strands are cut into sub-strands, sub-strands that partiallyor completely overlap other sub-strands (e.g., GGCTTA and TTAG). All ofthe smaller, randomized sub-strands may be sequenced at the same time,potentially after being amplified. In such applications, it will beappreciated that because the sub-strands do not represent the samesub-sequences, it may be desirable to detect RF signals generated (ornot generated) by each sensor 105 to detect MNPs because the sequencingof the sub-strands will not be coordinated (or synchronized) amongstsub-strands. For example, during a single sequencing cycle, a firstsub-strand may incorporate cytosine, a second sub-strand mightincorporate thymine, and a third sub-strand might incorporate adenine.In order to sequence multiple random segments of a larger nucleic acidstrand, it is desirable, in each sequencing cycle, to determine whetherand at which physical location(s) each dNTP type has been incorporated.Accordingly, when using the exemplary method 500 shown in FIG. 11 , thedecision at 510 may be “yes” for one sensor 105 after addition of aparticular nucleotide precursor and “no” for another. Thus, whensequencing randomized sub-strands of a nucleic acid such as DNA, it maybe desirable to test all four nucleotide precursors during eachsequencing cycle, even though for some of the sensors 105 the decisionat 510 is “yes” for the first, second, or third tested nucleotideprecursor.

Although FIG. 11 assumes that each of the nucleotide precursors islabeled by the same type of MNP, it is not a requirement to use the sametype of MNP for each of the nucleotide precursors. For example, it maybe convenient to use the same type of MNP for each of the nucleotideprecursors, but, alternatively, different nucleotide precursors may belabeled by different types of MNP. In other words, two or more of thenucleotide precursors may be labeled by the same type of MNP, or two ormore nucleotide precursors may be labeled by different types of MNP.

For example, various other embodiments are directed to using multipleMNP types (for example, MNP 1, 2, 3, and 4), each causing the sensor 105to generate a distinguishable RF signal. Focusing on the DNA example forillustration, each individual base (A, T, C, G) can be labeled by adifferent type of MNP (e.g., base A with MNP 1, base C with MNP 2, baseG with MNP 3, and base T with MNP 4) by either tagging each baseseparately and mixing them together or functionalizing each type of MNPdifferently so that it has an affinity for a particular (e.g., itsassigned) base. In a single chemistry run, all tagged(magnetically-labeled) bases may be introduced into a microfluidic cell(e.g., the fluidic channel 115 of the detection device 100) in which DNAstrands (e.g., fragments) to be sequenced have been attached within themicrofluidic cell (e.g., as described in the discussion above of thedetection devices 100).

After binding the target DNA strands to be sequenced to the detectiondevice 100, all four magnetically-labeled nucleotide precursors can beintroduced into the fluidic channel at the same time. Polymerase acts toincorporate nucleotide precursors that are complementary to those in thetarget strand. Changes in RF signals generated (or not generated) bySTOs of the detection device 100 can be used to identify which MNP (and,therefore, nucleotide precursor), if any, has been incorporated in thevicinity of each sensor 105. After each nucleotide precursor has beenintroduced in the fluidic channel(s) 115, and the sensors 105 have beenread, the MNPs may be cleaved from the incorporated magnetically-labelednucleotide precursor using, for example, enzymatic or chemical cleavage,as is known in the art. The process can then be repeated for the nextunpaired base in the strand being sequenced.

Accordingly, in some embodiments for DNA sequencing applications,instead of using a binary method with four chemistry steps for each baseread (sequencing cycle), four different MNPs, each causing the STO togenerate a distinguishable RF signal, can be used as the magneticlabels, and all of them can be detected in a single chemistry step. Forexample, each type of molecule (e.g., in DNA sequencing applications,each dNTP type) can be labeled by a different MNP type, where each MNPtype causes the STO to generate (or not generate) a RF signal having atleast one characteristic (e.g., frequency) enabling the presence orabsence of the MNP to be distinguished from all other MNPs being used asmagnetic labels. For example, in a DNA sequencing application, A can belabeled by MNP1, T by MNP2, C by MNP3, and G by MNP4, where thefrequencies of the RF signals generated by STOs influenced by MNP1,MNP2, MNP3, and MNP4 are all different enough that the three or fourtypes of MNPs can be distinguished by detecting whether the STO isgenerating (or has ceased to generate) a RF signal having specifiedcharacteristics (e.g., frequency). Detection circuitry 130 (e.g.,exemplary embodiments shown and described in the context of FIGS. 7A-10) can detect the frequency (or change in frequency) of the RF signalgenerated by each STO to identify which of the nucleotide precursors hasbeen incorporated into the DNA strand bound in the vicinity of andassociated with that STO.

For example, as explained above (see, e.g., the discussion of FIG. 7A),the detection circuitry 130 may include a tunable reference oscillator(RO) 610, and the detection circuitry 130 may sweep the frequency rangeof the RO 610 while measuring the STO signal. When the RO 610 frequencyis close to the STO frequency (e.g., using the circuit 600A of FIG. 7A),the DC output 620 is nonzero. It can be determined based on the nonzeroDC output 620 and the frequency of the RO 610 when the DC output 620 isnonzero what the frequency of the STO signal is. Knowing how the STOfrequency changes due to the magnetic fields emitted by the differentMNPs being used as labels, it can be determined which particle ispresent.

FIG. 12A illustrates a method 550 suitable for DNA sequencing usingMNP-labeled nucleotide precursors and a tunable reference oscillator 610in accordance with some embodiments. At 552, the method 550 begins. At554, each nucleotide precursor type (G, A, C, T) is labeled by adifferent MNP type (e.g., A by MNP1, T by MNP2, C by MNP3, and G byMNP4). At 556, nucleic acid strands to be sequenced, polymerasemolecules, and the MNP-labeled nucleotide precursors are introduced into the fluidic channel 115 of a detection device 100. After a period oftime suitable to allow incorporation of the nucleotide precursors, at558, the frequency of the reference oscillator is swept, and thedetection circuit (e.g., circuit 600A) determines the state of eachsensor 105 (e.g., some or all of the sensors 105 of the detection device100). At 560, each sensor 105's state (e.g., its output signal) isanalyzed/processed to identify which of the four MNP types was detectedat each of the sensors 105. The identity of the incorporated nucleotideprecursor can then be determined, and the identity of the paired base isknown and can be recorded. The method 550 ends at 562.

Alternatively, as also explained above (see, e.g., the discussion ofFIG. 7B), the detection circuitry 130 may include a plurality ofreference oscillators 610, each configured to generate a frequency thatis close to the frequency of the STO's RF signal in the presence of oneof the MNPs being used. During each sequencing cycle, after the fourMNP-labeled nucleotide precursors are introduced, a switch 611 may cyclethrough each RO 610, and the DC output 620 of the circuit 600B may bedetected as described in the discussion of FIG. 7B above. Once again,the DC output 620 should be nonzero only when the switch 611 isconnected to the RO 610 that is oscillating at approximately thefrequency of the STO. From this information, the identity of theparticle can be determined.

FIG. 12B illustrates a method 570 suitable for DNA sequencing usingMNP-labeled nucleotide precursors and a plurality of referenceoscillators 610 in accordance with some embodiments. FIG. 12B assumesthere are four MNPs in use and, accordingly, four reference oscillators610, but it is to be appreciated that there may be more or fewer thanfour reference oscillators 610. The method 570 begins at 572. At 574,each nucleotide precursor type (G, A, C, T) is labeled by a differentMNP type (e.g., A by MNP1, T by MNP2, C by MNP3, and G by MNP4). At 576,nucleic acid strands to be sequenced, polymerase molecules, and theMNP-labeled nucleotide precursors are introduced in to the fluidicchannel 115 of a detection device 100. After a period of time suitableto allow incorporation of the nucleotide precursors, at 578, a switch611 is set to connect to a first reference oscillator 610A (see FIG.7B). At 580, for each of one or more sensors 105 of a detection device100, it is determined whether the output of the detection circuit isnonzero or above a threshold. If so, then the detected MNP type isidentified, the identity of the paired base may be recorded at 594, andthe method 570 ends for that sensor 105 for the sequencing cycle. If theoutput of the detection circuit is zero or below the threshold, at 582,the switch 611 is set to connect to a second reference oscillator 610B(see FIG. 7B). At 584, it is determined whether the output of thedetection circuit is nonzero or above a threshold (which may be the sameas or different from the threshold used previously). If so, then thedetected MNP type is identified, the identity of the paired base may berecorded at 594, and the method 570 ends for that sensor 105 for thesequencing cycle. If the output of the detection circuit is zero orbelow the threshold, at 586, the switch 611 is set to connect to a thirdreference oscillator 610C (see FIG. 7B). At 588, it is determinedwhether the output of the detection circuit is nonzero or above athreshold (which may be the same as or different from the thresholdsused previously). If so, then the detected MNP type is identified, theidentity of the paired base may be recorded at 594, and the method 570ends for that sensor 105 for the sequencing cycle. If the output of thedetection circuit is zero or below a threshold, at 590, the switch 611is set to connect to a fourth reference oscillator 610D (see FIG. 7B).At 592, it is determined whether the output of the detection circuit isnonzero or above a threshold (which may be the same as or different fromthe thresholds used previously). If so, then the detected MNP type isidentified, the identity of the paired base may be recorded at 594, andthe method 570 ends for the sequencing cycle. If not, then the method570 ends at 596.

Methods of Fabricating Sensors and Detection Devices

In some embodiments, the detection device 100 is fabricated usingphotolithographic processes and thin film deposition. FIG. 13Aillustrates a method 850 of manufacturing the detection device 100, andFIG. 13B illustrates the results of steps of the fabrication method 850with a final panel showing polymerase bound to the wall 117 proximate toa sensor 105 in accordance with some embodiments (e.g., when thedetection device 100 is used for nucleic acid sequencing). At 852, themethod 850 begins. At 854, at least one line 120 is fabricated on asubstrate, for example, by depositing one or more metal layers, using,for example, photolithography to pattern an array of lines and spaces ina polymer layer applied on top of the metal layers, using that polymerlayer as a mask for etching the metal layers into an array of lines,depositing an insulating dielectric material, stripping the polymerlayer and dielectric material over the lines, and performing chemicalmechanical polishing to planarize the surface. At 856, the sensor array110 is fabricated on the at least one line 120. Each sensor 105 of thesensor array 110 has a bottom portion 108 and a top portion 109. (SeeFIG. 1A.) The bottom portion 108 is coupled to the at least one line120. In some embodiments, the bottom portion 108 of each sensor 105 isin contact with the at least one line 120.

At 858, dielectric material is deposited between the sensors 105 of thesensor array 110. At 860, additional lines 120 are fabricated. Each ofthese additional lines 120 is coupled to the top portion 109 of at leastone sensor 105 in the sensor array 110. In some embodiments, the topportion 109 of each sensor 105 is in contact with a line 120. In someembodiments, the bottom portion 108 of a sensor 105 is in contact with afirst line 120A, and the top portion 109 of the sensor 105 is in contactwith a second line 120B. At 862, a portion of the dielectric materialadjacent to the sensors 105 is removed (e.g., by milling, etching, orany other suitable removal process) to create the fluidic channel 115.At 864, the method 850 ends.

Electrical detection for DNA sequencing described in this disclosure mayprovide a variety of advantages over currently-used technologiesinvolving optical detection methods. For example, electrical detectionis not limited in terms of scaling flow cell dimensions in the samemanner that optical detection is limited due to optical imaging beingdiffraction limited. Magnetic detection is a form of electricaldetection for sequencing that has advantages over commonly proposedtunnel current detection schemes, because tunneling current methodsmeasure very small currents (which reduces SNR), and the tunnel junctionelements are exposed directly to the sequencing chemistries, which couldcause corrosion or other detrimental issues that degrade the accuracy ofthe sequencing process. By comparison, magnetic detection has largersignals (and better SNR) and can be performed without labeling particlesbeing in direct contact with the sensors 105, thereby allowing sensors105 to be coated in a protective layer that mitigates interactions withthe sequencing reagents.

For various embodiments described herein, the STO detection techniquescan be used in a relatively simple binary process to detect the presenceof an introduced DNA nucleotide precursor (e.g., via detection of afinite or approximately zero voltage at the output of an analogdetection circuit). As such, it can reduce the SNR needed to operate thedetection system at a high level of accuracy, which makes STO designeasier. It also provides flexibility in the choice of MNPs used aslabels for the molecules to be detected because only a small magneticfield without any particular field direction turns off or turns on theSTO. Thus, both superparamagnetic and ferromagnetic particles may beused without use of an external magnetic field to align particles atdifferent sites in the flow cell (e.g., sensor array 110).

Embodiments herein that use digital processing for detection may also beadvantageous to detect STO oscillation frequencies and/or changes in STOoscillation frequencies using reliable, accurate hardware components(e.g., ADCs and DSPs or other similar components) and well-understoodalgorithms (e.g., Fourier transforms or any other knownfrequency-analysis techniques to assess the frequency content of the RFsignal).

A limitation of magnetic detection may be the SNR of the sensor 105. Anadvantage of some of the disclosed embodiments is that the STO 604operates at a higher frequency and will thus have reduced 1/f noise,which results in reduced total noise. Another advantage is that becausea single voltage is detected at the output of the detector, use of STOs604 should be fast and should allow for high data collection throughput,which is desirable in detection systems (e.g., for DNA sequencing).

In the foregoing description and in the accompanying drawings, specificterminology has been set forth to provide a thorough understanding ofthe disclosed embodiments. In some instances, the terminology ordrawings may imply specific details that are not required to practicethe invention.

To avoid obscuring the present disclosure unnecessarily, well-knowncomponents are shown in block diagram form and/or are not discussed indetail or, in some cases, at all.

Unless otherwise specifically defined herein, all terms are to be giventheir broadest possible interpretation, including meanings implied fromthe specification and drawings and meanings understood by those skilledin the art and/or as defined in dictionaries, treatises, etc. As setforth explicitly herein, some terms may not comport with their ordinaryor customary meanings.

The terms “over,” “under,” “between,” “on,” and other similar terms asused herein refer to a relative position of one layer with respect toother layers. As such, for example, one layer disposed over or underanother layer may be directly in contact with the other layer or mayhave one or more intervening layers. Moreover, one layer disposedbetween layers may be directly in contact with the two layers or mayhave one or more intervening layers. In contrast, a first layer “on” asecond layer is in contact with the second layer. The relative positionof the terms does not define or limit the layers to a vector spaceorientation of the layers.

The terms “exemplary” and “embodiment” are used to express examples, notpreferences or requirements. Conditional language used herein, such as,among others, “can,” “could,” “might,” “may,” “e.g.,” and the like,unless specifically stated otherwise, or otherwise understood within thecontext as used, is generally intended to convey that certainembodiments include, while other embodiments do not include, certainfeatures, elements and/or steps. Thus, such conditional language is notgenerally intended to imply that features, elements and/or steps are inany way required for one or more embodiments or that one or moreembodiments necessarily include logic for deciding, with or withoutother input or prompting, whether these features, elements and/or stepsare included or are to be performed in any particular embodiment. Theterms “comprising,” “including,” “having,” and the like are synonymousand are used inclusively, in an open-ended fashion, and do not excludeadditional elements, features, acts, operations, and so forth. Also, theterm “or” is used in its inclusive sense (and not in its exclusivesense) so that when used, for example, to connect a list of elements,the term “or” means one, some, or all of the elements in the list.

Disjunctive language such as the phrases “at least one of X, Y, and Z,”“at least one of X, Y, or Z,” “one or more of X, Y, and Z,” and “one ormore of X, Y, or Z,” unless specifically stated otherwise, is otherwiseunderstood with the context as used in general to present that an item,term, etc., may be either X, Y, or Z, or any combination thereof (e.g.,X, Y, and/or Z). Thus, such disjunctive language is not generallyintended to, and should not, imply that certain embodiments require atleast one of X, at least one of Y, or at least one of Z to each bepresent.

Unless otherwise explicitly stated, articles such as “a” or “an” shouldgenerally be interpreted to include one or more described items.Accordingly, phrases such as “a device configured to” are intended toinclude one or more recited devices. Such one or more recited devicescan also be collectively configured to carry out the stated recitations.For example, “a processor configured to carry out recitations A, B andC” can include a first processor configured to carry out recitation Aworking in conjunction with a second processor configured to carry outrecitations B and C.

The drawings are not necessarily to scale, and the dimensions, shapes,and sizes of the features may differ substantially from how they aredepicted in the drawings.

While the above detailed description has shown, described, and pointedout novel features as applied to various embodiments, it can beunderstood that various omissions, substitutions, and changes in theform and details of the devices or algorithms illustrated can be madewithout departing from the spirit of the disclosure. As can berecognized, certain embodiments described herein can be embodied withina form that does not provide all of the features and benefits set forthherein, as some features can be used or practiced separately fromothers. The scope of certain embodiments disclosed herein is indicatedby the appended claims rather than by the foregoing description. Allchanges which come within the meaning and range of equivalency of theclaims are to be embraced within their scope. Accordingly, thespecification and drawings are to be regarded in an illustrative ratherthan a restrictive sense.

We claim:
 1. A method of distinguishing between labeled nucleotideprecursors using a detection device and at least two distinct groups ofmagnetic nanoparticles (MNPs), the detection device comprising aplurality of spin torque oscillators (STOs) and at least one fluidicchannel, the method comprising: labeling a first nucleotide precursorwith a first MNP, the first MNP being from a first group of the at leasttwo distinct groups of MNPs, the first group selected to cause amagnetization of each of the plurality of STOs to oscillate atapproximately a first frequency; labeling a second nucleotide precursorwith a second MNP, the second MNP being from a second group of the atleast two distinct groups of MNPs, the second group selected to causethe magnetization of each of the plurality of STOs to oscillate atapproximately a second frequency; adding the labeled first and secondnucleotide precursors to the fluidic channel of the detection device;detecting a frequency of a signal generated by at least one of theplurality of STOs; determining whether the frequency of the signalgenerated by the at least one of the plurality of the STOs matches thefirst frequency or the second frequency; and in response to thedetermining, identifying whether the first nucleotide precursor or thesecond nucleotide precursor has been detected.
 2. The method of claim 1,wherein detecting the frequency of the signal generated by the at leastone of the plurality of STOs comprises: collecting samples of the signalgenerated by the at least one of the plurality of STOs; and applying aFourier transform to the samples.
 3. The method of claim 1, whereindetecting the frequency of the signal generated by the at least one ofthe plurality of STOs comprises: collecting samples of the signalgenerated by the at least one of the plurality of STOs; and determiningfrequency content of the samples.
 4. The method of claim 1, whereindetecting the frequency of the signal generated by the at least one ofthe plurality of STOs comprises: multiplying the signal generated by theat least one of the plurality of STOs by a first reference signal ofapproximately the first frequency; and multiplying the signal generatedby the at least one of the plurality of STOs by a second referencesignal of approximately the second frequency, and wherein determiningwhether the frequency of the signal generated by the at least one of theplurality of the STOs matches the first frequency or the secondfrequency comprises: identifying the frequency of the signal generatedby the at least one of the plurality of STOs as the first frequency inresponse to a result of the multiplying being greater than a firstthreshold; and identifying the frequency of the signal generated by theat least one of the plurality of STOs as the second frequency inresponse to a result of the multiplying being greater than the firstthreshold or a second threshold.
 5. The method of claim 1, whereindetermining whether the frequency of the signal generated by the atleast one of the plurality of the STOs matches the first frequency orthe second frequency comprises determining whether the frequency of thesignal generated by the at least one of the plurality of STOs isapproximately the first frequency or approximately the second frequency.6. The method of claim 1, wherein determining whether the frequency ofthe signal generated by the at least one of the plurality of the STOsmatches the first frequency or the second frequency comprisesdetermining whether the frequency of the signal generated by the atleast one of the plurality of STOs is within a first frequency band orwithin a second frequency band, wherein the first frequency bandincludes the first frequency, and the second frequency band includes thesecond frequency.
 7. The method of claim 6, wherein the first frequencyband and the second frequency band are disjoint.
 8. The method of claim1, wherein detecting the frequency of the signal generated by the atleast one of the plurality of STOs is performed by a super-heterodynecircuit coupled to the at least one of the plurality of STOs.
 9. Themethod of claim 1, further comprising: in response to identifying thatthe first nucleotide precursor has been detected, recording an identityof the first nucleotide precursor or an identity of a base complementaryto the first nucleotide precursor, and/or in response to identifyingthat the second nucleotide precursor has been detected, recording anidentity of the second nucleotide precursor or an identity of a basecomplementary to the second nucleotide precursor.
 10. A method ofdetecting a labeled nucleotide precursor using a detection device, thedetection device comprising a plurality of spin torque oscillators(STOs) and at least one fluidic channel, the method comprising: labelinga nucleotide precursor with a magnetic nanoparticle (MNP); adding thelabeled nucleotide precursor to the fluidic channel of the detectiondevice; determining whether at least one of the plurality of STOs isgenerating a signal in a specified frequency band, wherein either (a)presence of the signal in the specified frequency band indicatespresence of the MNP or (b) presence of the signal in the specifiedfrequency band indicates absence of the MNP; and based at least in parton the determination of whether the at least one of the plurality ofSTOs is generating the signal in the specified frequency band,determining whether the labeled nucleotide precursor has been detected.11. The method of claim 10, wherein determining whether the at least oneof the plurality of STOs is generating the signal in the specifiedfrequency band comprises: detecting a presence or absence of a signal atan output of a super-heterodyne circuit coupled to the at least one ofthe plurality of STOs.
 12. The method of claim 10, further comprising:before adding the labeled nucleotide precursor to the fluidic channel ofthe detection device, binding at least one nucleic acid strand to abinding site in the fluidic channel, and adding, to the fluidic channel,an extendable primer and a plurality of molecules of nucleic acidpolymerase.
 13. The method of claim 10, further comprising: in responseto determining that the labeled nucleotide precursor has been detected,recording (a) an identity of the nucleotide precursor, or (b) anidentity of a base complementary to the labeled nucleotide precursor.14. An apparatus for molecule detection, the apparatus comprising: atleast one fluidic channel; a plurality of spin torque oscillators(STOs), each of the plurality of STOs configured to: (a) generate aradio-frequency (RF) signal in a specified frequency band in response todetecting a magnetic nanoparticle (MNP) labeling a molecule to bedetected within the at least one fluidic channel, or (b) cease togenerate the RF signal in the specified frequency band in response todetecting the MNP labeling the molecule to be detected within the atleast one fluidic channel; means for determining whether at least one ofthe plurality of STOs is generating the RF signal in the specifiedfrequency band; and means for determining, in response to determiningwhether the at least one of the plurality of STOs is generating the RFsignal in the specified frequency band, that the molecule to be detectedhas or has not been detected.
 15. The apparatus recited in claim 14,wherein the means for determining whether the at least one of theplurality of STOs is generating the RF signal comprises asuper-heterodyne circuit coupled to the at least one of the plurality ofSTOs.
 16. The apparatus recited in claim 14, wherein the means fordetermining whether the at least one of the plurality of STOs isgenerating the RF signal is configured to apply a DC current to the atleast one of the plurality of STOs.
 17. The apparatus recited in claim14, wherein the means for determining whether the at least one of theplurality of STOs is generating the RF signal comprises a referenceoscillator configured to generate a reference signal.
 18. The apparatusrecited in claim 17, wherein a frequency of the reference signal isselectable, and wherein the means for determining whether the at leastone of the plurality of STOs is generating the RF signal is configuredto select the frequency of the reference signal to substantially matchan expected oscillation frequency of the RF signal.
 19. The apparatusrecited in claim 14, wherein the means for determining whether the atleast one of the plurality of STOs is generating the RF signal isconfigured to mix a signal output from the at least one of the pluralityof STOs with a reference signal.
 20. The apparatus recited in claim 14,wherein the means for determining, in response to determining whetherthe at least one of the plurality of STOs is generating the RF signal,that the molecule to be detected has or has not been detected comprisesa processor.